Release Notes For GenBank Release 108

GBREL.TXT          Genetic Sequence Data Bank
                         15 August 1998

               NCBI-GenBank Flat File Release 108.0

                Distribution CD-ROM Release Notes

 2532359 loci,  1797137713 bases, from 2532359 reported sequences

  This document describes the format and content of the flat files that
comprise releases of the GenBank database. If you have any questions or
comments about GenBank or this document, please contact NCBI via email
at or:

   National Center for Biotechnology Information
   National Library of Medicine, 38A, 8N805
   8600 Rockville Pike
   Bethesda, MD  20894
   Phone:  (301) 496-2475
   Fax:    (301) 480-9241



1.1 Release 108.0
1.2 Cutoff Date
1.3 Important Changes in Release 108.0
1.4 Upcoming Changes
1.5 Request for Direct Submission of Sequence Data
1.6 Organization of This Document


2.1 Overview
2.2 Files
     2.2.1 File Descriptions
     2.2.5 File Sizes
     2.2.6 Per-Division Statistics 
     2.2.7 Selected Per-Organism Statistics 
     2.2.8 Growth of GenBank


3.1 File Header Information
3.2 Directory Files
     3.2.1 Short Directory File
3.3 Index Files
     3.3.1 Accession Number Index File
     3.3.2 Keyword Phrase Index File
     3.3.3 Author Name Index File
     3.3.4 Journal Citation Index File
     3.3.5 Gene Name Index
3.4 GenBank Data Submission Form and Error/Suggestion Report Form
3.5 Sequence Entry Files
     3.5.1 File Organization
     3.5.2  Entry Organization
     3.5.3 Sample Sequence Data File
     3.5.4 LOCUS Format
     3.5.5 DEFINITION Format
 DEFINITION Format for NLM Entries
     3.5.6 ACCESSION Format
     3.5.7 NID Format
     3.5.8 KEYWORDS Format
     3.5.9 SEGMENT Format
     3.5.10 SOURCE Format
     3.5.11 REFERENCE Format
     3.5.12 FEATURES Format
 Feature Key Names
 Feature Location
  Feature Qualifiers
 Cross-Reference Information
 Feature Table Examples
     3.5.13 ORIGIN Format
     3.5.14 SEQUENCE Format



5.1 Incorrect Gene Symbols in Entries and Index


6.1 Registered Trademark Notice
6.2 Citing GenBank
6.3 GenBank Distribution Formats and Media
6.4 Other Methods of Accessing GenBank Data
6.5 Request for Corrections and Comments
6.6 Credits and Acknowledgments
6.7 Disclaimer



1.1 Release 108.0

  The National Center for Biotechnology Information (NCBI) at the National
Library of Medicine (NLM), National Institutes of Health (NIH) is responsible
for producing and distributing the GenBank Sequence Database.  NCBI handles
all GenBank direct submissions and authors are advised to use the address
below.  Submitters are encouraged to use the free Sequin software package
for sending sequence data, or the newly developed World Wide Web submission
form.  See Section 1.5 below for details.


The address for direct submissions to GenBank is:

       GenBank Submissions
       National Center for Biotechnology Information
       Bldg 38A, Rm. 8N-803
       8600 Rockville Pike
       Bethesda, MD 20894


Updates and changes to existing GenBank records:


URL for the new GenBank submission tool - BankIt - on the World Wide Web:

(see Section 1.5 for additional details about submitting data to GenBank.)


  GenBank Release 108.0 is a release of sequence data by NCBI in the GenBank
flat file format.  GenBank is a component of a tri-partite, international
collaboration of sequence databases in the U.S., Europe, and Japan.  The
collaborating databases in Europe are the European Molecular Biology Laboratory
(EMBL) at Hinxton Hall, UK, and the DNA Database of Japan (DDBJ) in Mishima,
Japan. Sequence data is also incorporated from the Genome Sequence Data Base
(GSDB), Santa Fe, NM.  Patent sequences are incorporated through arrangements
with the U.S. Patent and Trademark Office, and via the collaborating
international databases from other international patent offices.  The database
is converted to various output formats, including the Flat File and Abstract
Syntax Notation 1 (ASN.1) versions.  The ASN.1 and Flat File forms of the data
are available at NCBI's anonymous FTP server: .

1.2 Cutoff Date

  This full release, 108.0, incorporates data available to the databases as of
August 10, 1998.  For more recent data, users are advised to download the
update files by anonymous FTP to '' or to search the updates via
the e-mail server.  For instructions on the use of the e-mail server, send 
mail message with the word 'help' in it to:

1.3 Important Changes in Release 108.0

1.3.1 Organizational changes

  Due to the growth in the number of EST sequences, the EST division is now
being split into 24 pieces.

1.4 Upcoming Changes

1.4.1 Relaxation of 350 kilobase limit

  During the May 1998 collaborative meeting among DDBJ, EMBL, and GenBank,
it was decided that the 350kb limit for the maximum number of bases within
a single database record would be relaxed in some special cases.

  One such case occurs when a single gene (eg, the human DMD gene) exceeds
350KB. Rather than splitting such a gene into multiple pieces, a single
record in the database will be used to represent the entire gene.

  Note that HTGS Phase 1 and Phase 2 sequences are another case in which
the 350kb limit may be exceeded, although once they transition to Phase 3
they *are* subject to the 350kb length limitation.

1.4.2 Sequence literals to be phased out

  Also agreed at the May 1998 collaborative meeting : the removal of
sequence 'literals' from the syntax for feature locations. Prior to
this decision, feature locations of the form:


have been legal. With this change, the use of literals (such as
atgcatgc in the example above) will no longer be supported. All entries
in the database that use sequence literals within feature locations
will be identified and fixed over the coming months. The target
date for their complete removal is October, 1998 (GenBank Release 109.0).

1.4.3 New REFERENCE type for on-line journals

  Agreement was reached at the May collaborative meeting that some
effort should be made to accomodate references which are published
only on-line. Until specifications for such references are available
from library organizations, GenBank will present them in a manner
like this:

	REFERENCE   1  (bases 1 to 2858)
	  AUTHORS   Smith, J.
	  TITLE     Cloning and expression of a phospholipase gene
	  JOURNAL   Online Publication
	  REMARK    Online-Journal-name; Article Identifier; URL

  This format is still tentative; additional information about this new
reference type will be made available via these release notes.

1.4.4 Selenocysteine representation

  Selenocysteine residues within the protein translations of coding
region features have been represented in GenBank via the letter 'X'
and a /transl_except qualifier. At the May collaborative meeting, it
was learned that IUPAC plans to adopt the letter 'U' for selenocysteine.

  DDBJ, EMBL, and GenBank will thus use this new amino acid abbreviation
for its /translation qualifiers. Although a timetable for its appearance
has not been decided upon, we are mentioning this now because the
introduction of a new residue abbreviation is a fairly fundamental change.
Details about the use of 'U' will be made available via these release
notes as they become available.

1.4.5 Miscellaneous qualifier changes

  Two new qualifiers, /plastid and /country, will be introduced starting
with GenBank Release 110.0 (December, 1998). Documentation for the format
and usage of these new qualifiers will be made available via these release
notes as they become available.

  In addition, the format of the cons_splice qualifier will be modified
such that the value "ABSENT" will be supported in addition to "YES" and
"NO". This change will accomodate 5'-partial or 3'-partial introns for
which sequence data is not available to determine whether a splice site
conforms to the consensus.

1.4.6 Additional files to be split into multiple pieces

  To simplify file management, the maximum size of GenBank sequence data
files is intended to be on the order of 250MB to 300MB. Thus, gbgss.seq,
gbbct.seq, and gbpln.seq are all likely to be split into two pieces starting
with release 108.0 . The gbgss.seq file, in particular, has experienced a
large unanticipated size increase.

1.4.7 Accession Number Format, NIDs, and PIDs

  With GenBank Release 81.0 (February, 1994) NCBI introduced an integer
identifier called a 'gi' for every sequence (DNA, RNA, protein translation)
in the database. The purpose of this identifer is to track a sequence as it
changes over time; a new gi is assigned to every sequence version, and
pointers between old and new gis are established. gis originally appeared
via the COMMENT and /note fields of the GenBank flatfile format.

  When DDBJ and EMBL introduced similar sequence tracking methods, the more
general terms 'nucleotide identifiers' (NIDs) and 'protein identifiers' (PIDs)
were adopted, and new linetypes and qualifiers were defined for these types
of identifiers.

  NIDs and PIDs have drawbacks, however. They are large integer values that
communicate no intrinsic meaning to database users. And they are really
internal database keys not easily amenable to collaborative maintenance. For
example, a protein translation issued a PID by DDBJ must still be assigned
a 'gi' when received by NCBI, which leads to two PID /db_xref qualifiers on
the corresponding CDS feature (one with a 'd' PID value and the other with
a 'g' PID value).

  For these reasons, DDBJ, EMBL, and GenBank have agreed to introduce a new
system of identifiers for *both* nucleotide and protein sequences, of the form
'Accession.Version' (eg, AB000349.3). The accession portion of these
identifiers is stable and will not change, but the version portion will be
incremented whenever the underlying sequence changes.

  Here is an example of how ACCESSION, NID, and /db_xref currently appear
in a typical GenBank entry:

LOCUS       AAU36846      568 bp    DNA             PRI       26-OCT-1995
DEFINITION  Aotus azarai cytochrome c oxidase subunit II (COII) gene,
            mitochondrial gene encoding mitochondrial protein, partial cds.
NID         g1040987
     CDS             <1..>568
                     /product="cytochrome c oxidase subunit II"

During transition to the Accession.Version system, a new VERSION
linetype and /protein_id qualifier will be introduced:

LOCUS       AAU36846      568 bp    DNA             PRI       26-OCT-1995
DEFINITION  Aotus azarai cytochrome c oxidase subunit II (COII) gene,
            mitochondrial gene encoding mitochondrial protein, partial cds.
NID         g1040987
VERSION     U36846.1  GI:1040987
     CDS             <1..>568
                     /product="cytochrome c oxidase subunit II"
                     /protein_id = "AAA12345.1"

And after the transition period is complete:

LOCUS       AAU36846      568 bp    DNA             PRI       26-OCT-1995
DEFINITION  Aotus azarai cytochrome c oxidase subunit II (COII) gene,
            mitochondrial gene encoding mitochondrial protein, partial cds.
VERSION     U36846.1  GI:1040987
     CDS             <1..>568
                     /product="cytochrome c oxidase subunit II"
                     /protein_id = "AAA12345.1"

  Note the eventual removal of NID and PID, and the preservation of
the ACCESSION linetype. Note also that, if you use NCBI gi identifiers
to link to NCBI systems, they will remain available via the VERSION
linetype and the type "GI" /db_xref qualifier.

  Detailed examples of the new accession number format and the manner in which
they will appear in GenBank flatfiles will be provided via upcoming GenBank
Release Notes and posts to the bionet.molbio.genbank newsgroup.

  DDBJ, EMBL, and GenBank plan to synchronize their release-processing
schedules so that a common close-of-data occurs on February 15, 1999.
In GenBank's case, this means that close-of-data for Release 111.0
will be delayed by approximately 2 weeks, and that the release itself
won't be available until near the end of the month.

  Database update files and releases generated after 2/15/99 are intended
to make use of the 'Accession.Version' format for both nucleotide and
protein sequences.

1.5 Request for Direct Submission of Sequence Data

  A successful GenBank requires that the data enter the database as soon
as possible after publication, that the annotations be as complete as
possible, and that the sequence and annotation data be accurate. All
three of these requirements are best met if authors of sequence data
submit their data directly to GenBank in a usable form. It is especially
important that these submissions be in computer-readable form.

  GenBank must rely on direct author submission of data to ensure that
it achieves its goals of completeness, accuracy, and timeliness. To
assist researchers in entering their own sequence data, GenBank
provides a WWW submission tool called BankIt, as well as a stand-alone
software package called Sequin. BankIt and Sequin are both easy-to-use
programs that enable authors to enter a sequence, annotate it, and
submit it to GenBank.  Through the international collaboration of DNA
sequence databases, GenBank submissions are forwarded daily for inclusion
in the EMBL and DDBJ databases.

  SEQUIN.  Sequin is an interactive, graphically-oriented program based
on screen forms and controlled vocabularies that guides you through the
process of entering your sequence and providing biological and
bibliographic annotation.  Intended as an alternative to the older
Authorin program, Sequin is designed to simplify the sequence submission
process, and to provide increased data handling capabilities to accomodate
very long sequences, complex annotations, and robust error checking.  E-mail
the completed submission file to :

  Sequin is currently provided as a beta-test version, and runs on
Macintosh, PC/Windows, UNIX and VMS computers. It is available by
annonymous ftp from , login as anonymous and use your
e-mail address as the password. It is located in the sequin directory.

  BANKIT.  BankIt provides a simple forms approach for submitting your
sequence and descriptive information to GenBank.  Your submission will
be submitted directly to GenBank via the World Wide Web, and
immediately forwarded for inclusion in the EMBL and DDBJ databases.
BankIt may be used with Netscape clients for Unix, Macs, and PCs, the
Mosaic client for Unix, and the MacWeb client for Macs. You can access
BankIt from GenBank's home page:

  AUTHORIN.  Authorin is no longer the primary means for submitting
sequences to GenBank, and is no longer being distributed by NCBI.  For
submitters who already have this program, however, we do continue to
accept Authorin submissions.

  For those who are unable to use Sequin or BankIt, GenBank has an ASCII
text electronic data submission form. This form is standardized among
EMBL, DDBJ, GenBank, PIR, MIPS, and JIPID.  The GenBank Data
Submission Form (located in the file GBDAT.FRM) can be used to submit
your sequence and annotations. Electronic mail submissions should go
to:  Direct mail on floppy disk should go to:

   GenBank Submissions
   National Center for Biotechnology Information
   Bldg. 38A, Rm 8N-803
   8600 Rockville Pike
   Bethesda, MD 20894

  If you have questions about GenBank submissions or any of the data
submission tools, contact NCBI at: or 301-496-2475.

1.6 Organization of This Document

  The second section describes the contents of GenBank releases. The third
section illustrates the formats of the flat files.  The fourth section
describes other versions of the data, the fifth section identifies known prob-
lems, and the sixth contains administrative details.


2.1 Overview

  GenBank releases consist of a set of ASCII text files, most of which
contain sequence data. A few supplemental "index" files are also supplied,
containing comprehensive lists of author names, journal citations,
gene names, and keywords, along with the accession numbers of the records
in which they can be found (see Section 3.3). The line-lengths of
these files is variable.

2.2 Files

  This GenBank flat file release consists of forty-eight files. The list
that follows describes each of the files included in the distribution.
Their sizes and base pair content are also summarized.

2.2.1 File Descriptions

 1. gbrel.txt 	- Release notes (this document).
 2. gbsdr.txt 	- Short directory of the data bank.
 3. gbacc.idx 	- Index of the entries according to accession number.
 4. gbkey.idx 	- Index of the entries according to keyword phrase.
 5. gbaut.idx 	- Index of the entries according to author.
 6. gbjou.idx 	- Index of the entries according to journal citation.
 7. gbgen.idx 	- Index of the entries according to gene names.
 8. gbdat.frm 	- Forms for submitting sequences or corrections to GenBank.
 9. gbpri1.seq 	- Primate sequence entries, part 1.
10. gbpri2.seq 	- Primate sequence entries, part 2.
11. gbrod.seq 	- Rodent sequence entries.
12. gbmam.seq 	- Other mammalian sequence entries.
13. gbvrt.seq 	- Other vertebrate sequence entries.
14. gbinv.seq 	- Invertebrate sequence entries.
15. gbpln.seq 	- Plant sequence entries (including fungi and algae).
16. gbbct.seq 	- Bacterial sequence entries.
17. gbrna.seq 	- Structural RNA sequence entries.
18. gbvrl.seq 	- Viral sequence entries.
19. gbphg.seq 	- Phage sequence entries.
20. gbsyn.seq 	- Synthetic and chimeric sequence entries.
21. gbuna.seq 	- Unannotated sequence entries.
22. gbest1.seq  - EST (expressed sequence tag) sequence entries, part 1.
23. gbest2.seq  - EST (expressed sequence tag) sequence entries, part 2.
24. gbest3.seq  - EST (expressed sequence tag) sequence entries, part 3.
25. gbest4.seq  - EST (expressed sequence tag) sequence entries, part 4.
26. gbest5.seq  - EST (expressed sequence tag) sequence entries, part 5.
27. gbest6.seq  - EST (expressed sequence tag) sequence entries, part 6.
28. gbest7.seq  - EST (expressed sequence tag) sequence entries, part 7.
29. gbest8.seq  - EST (expressed sequence tag) sequence entries, part 8.
30. gbest9.seq  - EST (expressed sequence tag) sequence entries, part 9.
31. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
32. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
33. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
34. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
35. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
36. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
37. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
38. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
39. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
40. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
41. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
42. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
43. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
44. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
45. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
46. gbpat.seq   - Patent sequence entries.
47. gbsts.seq   - STS (sequence tagged site) sequence entries.
48. gbgss.seq   - GSS (genome survey sequence) sequence entries.
49. gbhtg.seq   - HTGS (high throughput genomic sequencing) sequence entries.

2.2.5 File Sizes

  The following table indicates the approximate sizes of the individual files
in this release.  Since minor changes to some of the files may occur after the
release notes are written, these sizes should not be used to determine file
integrity; they are provided as an aid to planning only.

File Size      File Name

 92091214      gbacc.idx
1002822841     gbaut.idx
306576448      gbbct.seq
177675531      gbest1.seq
246465940      gbest10.seq
229606863      gbest11.seq
167444686      gbest12.seq
227131201      gbest13.seq
223018507      gbest14.seq
193419907      gbest15.seq
215037126      gbest16.seq
219533162      gbest17.seq
220680525      gbest18.seq
222152050      gbest19.seq
210829443      gbest2.seq
217904574      gbest20.seq
209984922      gbest21.seq
217366363      gbest22.seq
210565183      gbest23.seq
170415697      gbest24.seq
222028217      gbest3.seq
216799771      gbest4.seq
208855686      gbest5.seq
257135211      gbest6.seq
224785764      gbest7.seq
224507405      gbest8.seq
227643071      gbest9.seq
  8450879      gbgen.idx
525049370      gbgss.seq
227904761      gbhtg.seq
267024792      gbinv.seq
102058776      gbjou.idx
 82722693      gbkey.idx
 48048599      gbmam.seq
127619503      gbpat.seq
  7583111      gbphg.seq
299511516      gbpln.seq
144660193      gbpri1.seq
373484772      gbpri2.seq
    87541      gbrel.txt
  9465888      gbrna.seq
156044361      gbrod.seq
202591343      gbsdr.txt
157080711      gbsts.seq
 14637506      gbsyn.seq
  5063374      gbuna.seq
186285582      gbvrl.seq
 68919737      gbvrt.seq

2.2.6 Per-Division Statistics 

  The following table provides a per-division breakdown of the number of
sequence entries and the total number of bases of DNA/RNA in each sequence
data file:

Division     Entries         Bases

BCT            48000     120458258
EST1           74012      25241357
EST2           74000      27307291
EST3           74002      26800588
EST4           74000      27086986
EST5           74001      26990195
EST6           74000      27229304
EST7           74000      28237950
EST8           74000      28447664
EST9           74000      28512269
EST10          74000      22742718
EST11          74000      26405265
EST12          74000      24152186
EST13          74000      30259627
EST14          74000      27163217
EST15          74000      25920146
EST16          74000      28374827
EST17          74000      29335156
EST18          74000      31319085
EST19          74000      29377364
EST20          74000      28997047
EST21          74000      28239597
EST22          74000      29306986
EST23          74000      29994728
EST24          63845      25679203
GSS           222573     103970022
HTG             1321     176624900
INV            37044     134042870
MAM            15637      14792888
PAT           106218      33169128
PHG             1365       2748196
PLN            57550     126459385
PRI1           47630      45184241
PRI2           38398     214717002
RNA             4754       2451595
ROD            42067      55416169
STS            60564      21523617
SYN             2930       6712273
UNA             1918       1518671
VRL            56558      52692759
VRT            21972      21534983

2.2.7 Selected Per-Organism Statistics 

  The following table provides the number of entries and bases of DNA/RNA for
the twenty most sequenced organisms in Release 108.0 (chloroplast and mitochon-
drial sequences not included):

Entries      Bases   Species

1272266  742747641   Homo sapiens
356070   167900333   Mus musculus
76306    134214064   Caenorhabditis elegans
65913     63921921   Arabidopsis thaliana
43080     50224577   Drosophila melanogaster
10542     28616688   Saccharomyces cerevisiae
29335     21839544   Rattus norvegicus
4880      17686666   Escherichia coli
25764     13137932   Fugu rubripes
29539     11556585   Oryza sativa
23417     10379390   Human immunodeficiency virus type 1
1079       9862395   Bacillus subtilis
21715      8931870   Rattus sp.
1374       8470393   Schizosaccharomyces pombe
646        5750841   Mycobacterium tuberculosis
4755       5520114   Gallus gallus
14439      5357793   Brugia malayi
4451       4758578   Plasmodium falciparum
4991       4469170   Bos taurus
10840      4396447   Toxoplasma gondii

2.2.8 Growth of GenBank

  The following table lists the number of bases and the number of sequence
records in each release of GenBank, beginning with Release 3 in 1982.
Over the period 1982 to the present, the number of bases in GenBank
has doubled approximately every 14 months.

Release    Date     Base Pairs   Entries

    3    Dec 82         680338       606
   14    Nov 83        2274029      2427
   20    May 84        3002088      3665
   24    Sep 84        3323270      4135
   25    Oct 84        3368765      4175
   26    Nov 84        3689752      4393
   32    May 85        4211931      4954
   36    Sep 85        5204420      5700
   40    Feb 86        5925429      6642
   42    May 86        6765476      7416
   44    Aug 86        8442357      8823
   46    Nov 86        9615371      9978
   48    Feb 87       10961380     10913
   50    May 87       13048473     12534
   52    Aug 87       14855145     14020
   53    Sep 87       15514776     14584
   54    Dec 87       16752872     15465
   55    Mar 88       19156002     17047
   56    Jun 88       20795279     18226
   57    Sep 88       22019698     19044
   57.1  Oct 88       23800000     20579
   58    Dec 88       24690876     21248
   59    Mar 89       26382491     22479
   60    Jun 89       31808784     26317
   61    Sep 89       34762585     28791
   62    Dec 89       37183950     31229
   63    Mar 90       40127752     33377
   64    Jun 90       42495893     35100
   65    Sep 90       49179285     39533
   66    Dec 90       51306092     41057
   67    Mar 91       55169276     43903
   68    Jun 91       65868799     51418
   69    Sep 91       71947426     55627
   70    Dec 91       77337678     58952
   71    Mar 92       83894652     65100
   72    Jun 92       92160761     71280
   73    Sep 92      101008486     78608
   74    Dec 92      120242234     97084
   75    Feb 93      126212259    106684
   76    Apr 93      129968355    111911
   77    Jun 93      138904393    120134
   78    Aug 93      147215633    131328
   79    Oct 93      157152442    143492
   80    Dec 93      163802597    150744
   81    Feb 94      173261500    162946
   82    Apr 94      180589455    169896
   83    Jun 94      191393939    182753
   84    Aug 94      201815802    196703
   85    Oct 94      217102462    215273
   86    Dec 94      230485928    237775
   87    Feb 95      248499214    269478
   88    Apr 95      286094556    352414
   89    Jun 95      318624568    425211
   90    Aug 95      353713490    492483
   91    Oct 95      384939485    555694
   92    Dec 95      425860958    620765
   93    Feb 96      463758833    685693
   94    Apr 96      499127741    744295
   95    Jun 96      551750920    835487
   96    Aug 96      602072354    920588
   97    Oct 96      651972984    1021211
   98    Dec 96      730552938    1114581
   99    Feb 97      786898138    1192505
   100   Apr 97      842864309    1274747
   101   Jun 97      966993087    1491069
   102   Aug 97     1053474516    1610848
   103   Oct 97     1160300687    1765847
   104   Dec 97     1258290513    1891953
   105   Feb 98     1372368913    2042325
   106   Apr 98     1502542306    2209232
   107   Jun 98     1622041465    2355928
   108   Aug 98     1797137713    2532359


  The flat file examples included in this section, while not always from the
current release, are usually quite recent.  Any differences compared to the
actual data files are the result of updates to the entries involved.

3.1 File Header Information

  Each of the forty-eight files of a GenBank release begins with the
same header, except for the first line, which contains the file name,
and the sixth line, which contains the title of the file. The first
line of the file contains the file name in character positions 1 to 9
and the full data bank name (Genetic Sequence Data Bank) starting in
column 20. The brief names of the files in this release are listed in
section 2.2.

  The second line contains the date of the current release in the form
`day month year', beginning in position 26. The fourth line contains
the current GenBank release number. The release number appears in
positions 41 to 45 and consists of two numbers separated by a decimal
point. The number to the left of the decimal is the major release
number. The digit to the right of the decimal indicates the version of
the major release; it is zero for the first version. The sixth line
contains a title for the file. The eighth line lists the number of
entries (loci), number of bases (or base pairs), and number of reports
of sequences (equal to number of entries in this case). These numbers are
right-justified at fixed positions. The number of entries appears in
positions 1 to 7, the number of bases in positions 15 to 23, and the
number of reports in positions 37 to 40. (There are more reports of
sequences than entries since reported sequences that overlap or
duplicate each other are combined into single entries.) The third,
fifth, seventh, and ninth lines are blank.

1       10        20        30        40        50        60        70       79
GBACC.IDX          Genetic Sequence Data Bank
                         15 December 1993

                 GenBank Flat File Release 80.0

                      Accession Number Index

  150744 loci, 163802597 bases, from 150744 reported sequences
1       10        20        30        40        50        60        70       79

Example 1. Sample File Header

3.2 Directory Files

3.2.1 Short Directory File

  The short directory file contains brief descriptions of all of the
sequence entries contained in this release. These descriptions are in
fifteen groups, one group for each of the fifteen sequence entry
data files. The first record at the beginning of a group of entries
contains the name of the group in uppercase characters, beginning in
position 21. The organism groups are PRIMATE, RODENT, OTHER MAMMAL,
SEQUENCE TAGGED SITE.  The second record is blank.

  Each record in the short directory contains the sequence entry name
(LOCUS) in the first 12 positions, followed by a brief definition of
the sequence beginning in column 13. The definition is truncated (at
the end of a word) to leave room at the right margin for at least one
space, the sequence length, and the letters `bp'. The length of the
sequence is printed right-justified to column 77, followed by the
letters `bp' in columns 78 and 79. The next-to-last record for a group
has `ZZZZZZZZZZ' in its first ten positions (where the entry name
would normally appear). The last record is a blank line. An example of
the short directory file format, showing the descriptions of the last
entries in the Other Vertebrate sequence data file and the first
entries of the Invertebrate sequence data file, is reproduced below:

1       10        20        30        40        50        60        70       79
ZEFWNT1G3   B.rerio wnt-1 gene (exon 3) for wnt-1 protein.                266bp
ZEFWNT1G4   B.rerio wnt-1 gene (exon 4) for wnt-1 protein.                647bp
ZEFZF54     Zebrafish homeotic gene ZF-54.                                246bp
ZEFZFEN     Zebrafish engrailed-like homeobox sequence.                   327bp

AAHAV33A    Acanthocheilonema viteae pepsin-inhibitor-like-protein       1048bp
ACAAC01     Acanthamoeba castelani gene encoding actin I.                1571bp
ACAACTPH    Acanthamoeba castellanii actophorin mRNA, complete cds.       671bp
ACAMHCA     A.castellanii non-muscle myosin heavy chain gene, partial    5894bp
1       10        20        30        40        50        60        70       79
Example 2. Short Directory File

3.3 Index Files

There are five files containing indices to the entries in this release:

 Accession number index file
 Keyword phrase index file
 Author name index file
 Journal citation index file
 Gene name index file

  The index keys (accession numbers, keywords, authors, journals, and
gene symbols.) of an index are sorted alphabetically. (The index keys
for the keyword phrases and author names appear in uppercase
characters even though they appear in mixed case in the sequence
entries.) Under each index key, the names of the sequence entries
containing that index key are listed alphabetically. Each sequence
name is also followed by its data file division and primary accession
number. The following codes are used to designate the data file

 1. PRI - primate sequences
 2. ROD - rodent sequences
 3. MAM - other mammalian sequences
 4. VRT - other vertebrate sequences
 5. INV - invertebrate sequences
 6. PLN - plant, fungal, and algal sequences
 7. BCT - bacterial sequences
 8. RNA - structural RNA sequences
 9. VRL - viral sequences
10. PHG - bacteriophage sequences
11. SYN - synthetic sequences
12. UNA - unannotated sequences
13. EST - EST sequences (expressed sequence tags) 
14. PAT - patent sequences
15. STS - STS sequences (sequence tagged sites) 
16. GSS - GSS sequences (genome survey sequences) 
17. HTG - HTGS sequences (high throughput genomic sequences) 

  The index key begins in column 1 of a record. An 11-character field
for the sequence entry name starts in position 14 of a record,
followed by a 3-character field for the data file division, starting
at position 25 and ending at position 27, and a 6-character field for
the primary accession number, starting at position 29 and ending at
position 34. All entries in the fields are left-justified.

  Beginning at positions 36 and 58, the three fields repeat, so three
sets of sequence information can appear in one record. If there are
more than three entry names, the next records are used; the index key
is not repeated. For the accession number files, the entry names begin
in the same record as the index key, since the key is always less than
12 characters. In the other index files, the entry names begin on the
record following the index key record.

NOTE: The column positions stated above will be shifted to the
right if primary accessions in the 8-character format are present.

3.3.1 Accession Number Index File

  Accession numbers are unique six character or eight-character alphanumeric
identifiers of GenBank database entries. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits.  Accessions provide an unchanging identifier
for the data with which they are associated, and we encourage you to cite
accession numbers whenever you refer to data from GenBank.

  GenBank entries can have both 'primary' and 'secondary' accessions
associated with them (see Section 3.5.6).

  The following excerpt from the accession number index file illustrates
the format of the index:

1       10        20        30        40        50        60        70       79
J00316       HUMTBB11P  PRI J00316
J00317       HUMTBB46P  PRI J00317
J00318       HUMUG1     PRI J00318
J00319       HUMUG1PA   PRI J00319
J00320       HUMVIPMR1  PRI L00154 HUMVIPMR2  PRI L00155 HUMVIPMR3  PRI L00156
             HUMVIPMR4  PRI L00157 HUMVIPMR5  PRI L00158
J00321       BABA1AT    PRI J00321
J00322       CHPRSA     PRI J00322
J00323       AGMRSASPC  PRI J00323
J00324       BABATIII   PRI J00324
1       10        20        30        40        50        60        70       79

Example 4. Accession Number Index File

  If the same accession number is found in more than one entry (a result
of the infrequent occasions when a single entry is split into two or
more separate entries), then the additional entries and groups in
which the number appears are also given. In the example above, J00320
is a secondary accession, appearing on 5 other database entries.

3.3.2 Keyword Phrase Index File

  Keyword phrases consist of names for gene products and other
characteristics of sequence entries. There are approximately 18,000
keyword phrases. An excerpt from the keyword phrase index file is
shown below:

1       10        20        30        40        50        60        70       79
             ECOHELIV   BCT J04726 ECOUVRD    BCT X00738 FPLTRAX    BCT M38047
             HS2ULL     VRL D10470 HSECOMGEN  VRL M86664 PT4DDA     PHG M93048
             SYNPMMB190 SYN M37846 YSPRHP3    PLN X64583
             ECOPTRAI5  BCT X57430
             ECOUVRD2   BCT D00069 HEAMUTB1A  BCT M99049
             ECOP15BG   BCT X62121
             ECOPIN     BCT K00676 ECOPIN1    BCT X01805 PMUGINMOM  PHG V01463
             STABINR3   BCT X16298 STAINVSA   BCT M36694
             MSGDNAJHSP BCT M95576
             ECOLIG     BCT M24278 ECOLIGA    BCT M30255 PT4G30     PHG X00039
             PT6LIG55   PHG M38465 TTHDNALGS  BCT M74792 TTHDNALIG  BCT M36417
             VACCDNLIG  VRL X16512 VACRHF     VRL D11079 YSCCDC9    PLN X03246
             YSPCDC17   PLN X05107 ZMOLIG     BCT Z11910
1       10        20        30        40        50        60        70       79

Example 5. Keyword Phrase Index File

3.3.3 Author Name Index File

The author name index file lists all of the author names that appear
in the citations. An excerpt from the author name index file is shown

1       10        20        30        40        50        60        70       79
             RATLCAG1   ROD M18349 RATLCAG2   ROD M18348 RATLCAG3   ROD M18347
             RATLCAI    ROD M25820 RATLCAII   ROD M25821 RATLCAIII  ROD M25822
             RATLCAIV   ROD M25823 RATLCAR    ROD Y00065
             DRO16883C  INV X62939 DRO1688ED  INV X62938 DRO1688EP  INV X62937
             DROPER     INV M11969 DROPES     INV X03636 MUSPER     ROD M12039
             MUSURFPER  ROD X02966
             MUSHOMA    ROD X03033 MUSNEORP8R ROD X54812 MUSP7H2    ROD X54811
             MUSRPT     ROD M69041 MUSSOFI    ROD X63350 MUSTRP15   ROD X59513
             MUSTYRP2   ROD X63349
             RATTRH     ROD M12138
             DROFPS85D  INV X52844 MUSIGKAC3  ROD K00885 MUSIL4RA   ROD M27959
             MUSIL4RB   ROD M27960 RABGLOBCON MAM L05833 RABGLOBHSB MAM L05835
1       10        20        30        40        50        60        70       79

Example 6. Author Name Index File

3.3.4 Journal Citation Index File

  The journal citation index file lists all of the citations that appear
in the references. All citations are truncated to 80 characters. An
excerpt from the citation index file is shown below:

1       10        20        30        40        50        60        70       79
             HUMIGHVX   PRI M35415
             RANCRYG2A  VRT K02264 RANCRYG4A  VRT K02266 RANCRYG5A  VRT M22529
             RANCRYG6A  VRT M22530 RANCRYR    VRT X00659
             ECOTRXA1   BCT M54881
             BOVTRNB2A  MAM M36431 HUMTRNB    PRI M36429 HUMTRNB1   PRI M36430
             PFAHGPRT   INV M54896
             LAMCG      PHG J02459
ACTA BIOCHIM. BIOPHYS. SIN. 23, 246-253 (1992)
             HUMPLASINS PRI M98056
1       10        20        30        40        50        60        70       79

Example 7. Journal Citation Index File

3.3.5 Gene Name Index

  The /gene qualifiers of many GenBank entries contain values other than
official gene symbols, such as the product or the standard name of the gene.
Hence, NCBI has chosen to build an index (gbgen.idx) more like a keyword index
for this field, using both the GenBank /gene qualifier and the ''
fields from the NCBI internal database as keys. An excerpt from the gene name
index file is shown below:

1       10        20        30        40        50        60        70       79
             DROSUSG    INV M57889
             DROS2ZSTG  INV X56798
             DROS2ZSTM  INV X56799
             CHKSRVCNTK VRT M57290
             ARFSURCG   BCT X63435
1       10        20        30        40        50        60        70       79

Example 8. Gene Name Index File

3.4 GenBank Data Submission Form and Error/Suggestion Report Form

  The recommended methods for submitting sequence data to GenBank are via
BankIt and the Sequin program.  Please see Section 1.5 of this document for
further details.

  If it is not possible to use BankIt or Sequin, there is a data submission
form in this distribution (GBDAT.FRM) which can be filled out with a text
editor and returned to the database, preferably by e-mail.

  Direct submission e-mail address:

  The second form in the GBDAT.FRM is the GenBank Error/Suggestion Report
Form. It is separated from the Data Submission Form by a form-feed
character (<CTRL>L, ASCII octal value 014, ASCII decimal value 12). We
encourage all users to report any errors to the data bank staff
using this form. Like the GenBank Data Submission Form, it may be
printed and filled in by hand and sent by mail to the address given
at the beginning of the form. It may also be filled out using a text
editor and sent to GenBank by electronic mail at:

3.5 Sequence Entry Files

  GenBank releases contain forty sequence entry data files, one
for each "division" of GenBank.

3.5.1 File Organization

  Each of these files has the same format and consists of two parts:
header information (described in section 3.1) and sequence entries for
that division (described in the following sections).

3.5.2  Entry Organization

  In the second portion of a sequence entry file (containing the
sequence entries for that division), each record (line) consists of
two parts. The first part is found in positions 1 to 10 and may

1. A keyword, beginning in column 1 of the record (e.g., REFERENCE is
a keyword).

2. A subkeyword beginning in column 3, with columns 1 and 2 blank
(e.g., AUTHORS is a subkeyword of REFERENCE).

3. Blank characters, indicating that this record is a continuation of
the information under the keyword or subkeyword above it.

4. A code, beginning in column 5, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section below.

5. A number, ending in column 9 of the record. This number occurs in
the portion of the entry describing the actual nucleotide sequence and
designates the numbering of sequence positions.

6. Two slashes (//) in positions 1 and 2, marking the end of an entry.

  The second part of each sequence entry record contains the information
appropriate to its keyword, in positions 13 to 80 for keywords and
positions 11 to 80 for the sequence.

  The following is a brief description of each entry field. Detailed
information about each field may be found in Sections 3.5.4 to 3.5.14.

LOCUS	- A short mnemonic name for the entry, chosen to suggest the
sequence's definition. Mandatory keyword/exactly one record.

DEFINITION	- A concise description of the sequence. Mandatory
keyword/one or more records.

ACCESSION	- The primary accession number is a unique, unchanging
code assigned to each entry. (Please use this code when citing
information from GenBank.) Mandatory keyword/one or more records.

NID	- The unique nucleic acid identifier that has been assigned to
the current version of the sequence data that are associated with
the GenBank entry identified by a given primary accession number.

KEYWORDS	- Short phrases describing gene products and other
information about an entry. Mandatory keyword in all annotated
entries/one or more records.

SEGMENT	- Information on the order in which this entry appears in a
series of discontinuous sequences from the same molecule. Optional
keyword (only in segmented entries)/exactly one record.

SOURCE	- Common name of the organism or the name most frequently used
in the literature. Mandatory keyword in all annotated entries/one or
more records/includes one subkeyword.

   ORGANISM	- Formal scientific name of the organism (first line)
and taxonomic classification levels (second and subsequent lines).
Mandatory subkeyword in all annotated entries/two or more records.

REFERENCE	- Citations for all articles containing data reported
in this entry. Includes four subkeywords and may repeat. Mandatory
keyword/one or more records.

   AUTHORS	- Lists the authors of the citation. Mandatory
subkeyword/one or more records.

   TITLE	- Full title of citation. Optional subkeyword (present
in all but unpublished citations)/one or more records.

   JOURNAL	- Lists the journal name, volume, year, and page
numbers of the citation. Mandatory subkeyword/one or more records.

   MEDLINE	- Provides the Medline unique identifier for a
citation. Optional subkeyword/one record.

   REMARK	- Specifies the relevance of a citation to an
entry. Optional subkeyword/one or more records.

COMMENT	- Cross-references to other sequence entries, comparisons to
other collections, notes of changes in LOCUS names, and other remarks.
Optional keyword/one or more records/may include blank records.

FEATURES	- Table containing information on portions of the
sequence that code for proteins and RNA molecules and information on
experimentally determined sites of biological significance. Optional
keyword/one or more records.

BASE COUNT	- Summary of the number of occurrences of each base
code in the sequence. Mandatory keyword/exactly one record.

ORIGIN	- Specification of how the first base of the reported sequence
is operationally located within the genome. Where possible, this
includes its location within a larger genetic map. Mandatory
keyword/exactly one record.

	- The ORIGIN line is followed by sequence data (multiple records).

// 	- Entry termination symbol. Mandatory at the end of an
entry/exactly one record.

3.5.3 Sample Sequence Data File

  An example of a complete sequence entry file follows. (This example
has only two entries.) Note that in this example, as throughout the
data bank, numbers in square brackets indicate items in the REFERENCE
list. For example, in ACARR58S, [1] refers to the paper by Mackay, et

1       10        20        30        40        50        60        70       79
GBSMP.SEQ          Genetic Sequence Data Bank
                         15 December 1992

                 GenBank Flat File Release 74.0

                     Structural RNA Sequences

      2 loci,       236 bases, from     2 reported sequences

LOCUS       AAURRA        118 bp ss-rRNA            RNA       16-JUN-1986
DEFINITION  A.auricula-judae (mushroom) 5S ribosomal RNA.
KEYWORDS    5S ribosomal RNA; ribosomal RNA.
SOURCE      A.auricula-judae (mushroom) ribosomal RNA.
  ORGANISM  Auricularia auricula-judae
            Eukaryota; Fungi; Eumycota; Basidiomycotina; Phragmobasidiomycetes;
            Heterobasidiomycetidae; Auriculariales; Auriculariaceae.
REFERENCE   1  (bases 1 to 118)
  AUTHORS   Huysmans,E., Dams,E., Vandenberghe,A. and De Wachter,R.
  TITLE     The nucleotide sequences of the 5S rRNAs of four mushrooms and
            their use in studying the phylogenetic position of basidiomycetes
            among the eukaryotes
  JOURNAL   Nucleic Acids Res. 11, 2871-2880 (1983)
FEATURES             Location/Qualifiers
     rRNA            1..118
                     /note="5S ribosomal RNA"
BASE COUNT       27 a     34 c     34 g     23 t
ORIGIN      5' end of mature rRNA.
        1 atccacggcc ataggactct gaaagcactg catcccgtcc gatctgcaaa gttaaccaga
       61 gtaccgccca gttagtacca cggtggggga ccacgcggga atcctgggtg ctgtggtt
LOCUS       ABCRRAA       118 bp ss-rRNA            RNA       15-SEP-1990
DEFINITION  Acetobacter sp. (strain MB 58) 5S ribosomal RNA, complete sequence.
KEYWORDS    5S ribosomal RNA.
SOURCE      Acetobacter sp. (strain MB 58) rRNA.
  ORGANISM  Acetobacter sp.
            Prokaryotae; Gracilicutes; Scotobacteria; Aerobic rods and cocci;
REFERENCE   1  (bases 1 to 118)
  AUTHORS   Bulygina,E.S., Galchenko,V.F., Govorukhina,N.I., Netrusov,A.I.,
            Nikitin,D.I., Trotsenko,Y.A. and Chumakov,K.M.
  TITLE     Taxonomic studies of methylotrophic bacteria by 5S ribosomal RNA
  JOURNAL   J. Gen. Microbiol. 136, 441-446 (1990)
FEATURES             Location/Qualifiers
     rRNA            1..118
                     /note="5S ribosomal RNA"
BASE COUNT       27 a     40 c     32 g     17 t      2 others
        1 gatctggtgg ccatggcggg agcaaatcag ccgatcccat cccgaactcg gccgtcaaat
       61 gccccagcgc ccatgatact ctgcctcaag gcacggaaaa gtcggtcgcc gccagayy
1       10        20        30        40        50        60        70       79

Example 9. Sample Sequence Data File

3.5.4 LOCUS Format

  The pieces of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always ten characters or less, begins in position 13. The locus name
is designed to help group entries with similar sequences: the first
three characters usually designate the organism; the fourth and fifth
characters can be used to show other group designations, such as gene
product; for segmented entries the last character is one of a series
of sequential integers.

  The number of bases or base pairs in the sequence ends in position 29.
The letters `bp' are in positions 31 to 32. Positions 34 to 36 give
the number of strands of the sequence. Positions 37 to 40 give the
topology of molecule sequenced. If the sequence is of a special type,
a notation (such as `circular') is included in positions 43 to 52.

  GenBank sequence entries are divided among fifteen taxonomic
divisions. Each entry's division is identified by a three-letter code
in positions 53 to 55. See Section 3.3 for the division codes.

  Positions 63 to 73 of the record contain the date the entry was
entered or underwent any substantial revisions, such as the addition
of newly published data, in the form dd-MMM-yyyy.

The detailed format for the LOCUS record is as follows:

Positions   	Contents

1-12	LOCUS
13-22	Locus name
23-29	Length of sequence, right-justified
31-32	bp
34-36	Blank, ss- (single-stranded), ds- (double-stranded), or
	 ms- (mixed-stranded)
37-40	Blank, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA), 
	mRNA (messenger RNA), or uRNA (small nuclear RNA)
43-52	Blank (implies linear) or circular
53-55	The division code (see Section 3.3)
63-73	Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)

3.5.5 DEFINITION Format

  The DEFINITION record gives a brief description of the sequence,
proceeding from general to specific. It starts with the common name of
the source organism, then gives the criteria by which this sequence is
distinguished from the remainder of the source genome, such as the
gene name and what it codes for, or the protein name and mRNA, or some
description of the sequence's function (if the sequence is
non-coding). If the sequence has a coding region, the description may
be followed by a completeness qualifier, such as cds (complete coding
sequence). There is no limit on the number of lines that may be part
of the DEFINITION.  The last line must end with a period. DEFINITION Format for NLM Entries

  The DEFINITION line for entries derived from journal-scanning at the NLM is
an automatically generated descriptive summary that accompanies each DNA and
protein sequence. It contains information derived from fields in a database 
that summarize the most important attributes of the sequence.  The DEFINITION
lines are designed to supplement the accession number and the sequence itself
as a means of uniquely and completely specifying DNA and protein sequences. The
following are examples of NLM DEFINITION lines:

NADP-specific isocitrate dehydrogenase [swine, mRNA, 1 gene, 1585 nt]

94 kda fiber cell beaded-filament structural protein [rats, lens, mRNA
Partial, 1 gene, 1873 nt]

inhibin alpha {promoter and exons} [mice, Genomic, 1 gene, 1102 nt, segment
1 of 2]

cefEF, cefG=acetyl coenzyme A:deacetylcephalosporin C o-acetyltransferase
[Acremonium chrysogenum, Genomic, 2 genes, 2639 nt]

myogenic factor 3, qmf3=helix-loop-helix protein [Japanese quails,
embryo, Peptide Partial, 246 aa]

  The first part of the definition line contains information describing
the genes and proteins represented by the molecular sequences.  This can
be gene locus names, protein names and descriptions that replace or augment
actual names.  Gene and gene product are linked by "=".  Any special
identifying terms are presented within brackets, such as: {promoter},
{N-terminal}, {EC}, {alternatively spliced}, or {3' region}.

  The second part of the definition line is delimited by square brackets, '[]',
and provides details about the molecule type and length.  The biological
source, i.e., genus and species or common name as cited by the author.
Developmental stage, tissue type and strain are included if available.
The molecule types include: Genomic, mRNA, Peptide. and Other Genomic
Material. Genomic molecules are assumed to be partial sequence unless
"Complete" is specified, whereas mRNA and peptide molecules are assumed
to be complete unless "Partial" is noted.

3.5.6 ACCESSION Format

  This field contains a series of six-character and/or eight-character
identifiers called 'accession numbers'. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. The 'primary', or first, of the accession
numbers occupies positions 13 to 18 (6-character format) or positions
13 to 20 (8-character format). Subsequent 'secondary' accession numbers
(if present) are separated from the primary, and from each other, by a
single space. In some cases, multiple lines of secondary accession
numbers might be present, starting at position 13.

  The primary accession number of a GenBank entry provides a stable identifier
for the biological object that the entry represents. Accessions do not change
when the underlying sequence data or associated features change.

  Secondary accession numbers arise for a number of reasons. For example, a
single accession number may initially be assigned to a sequence from a
publication. If it is later discovered that the sequence must be entered into
the database as multiple entries, each entry would receive a new primary
accession number, and the original accession number would appear as a secondary
accession number on each of the new entries.

3.5.7 NID Format

  This field contains the unique nucleic acid sequence identifier that is
assigned by NCBI to the sequence data in a GenBank entry. Nucleic acid
identifiers consist of the letter 'g', followed by one or more digits. This
sequence identifier occupies positions 13 and higher.

  While accession numbers allow one to retrieve the same biological entry
in the database, regardless of changes to that record, the nucleic acid
identifier changes every time that the underlying sequence changes. Reasons
for sequence changes include: the removal of vector contamination, re-sequencing
of stretches of ambiguous sequence, and the correction of sequencing errors.

  At the NCBI, these nucleic acid sequence identifiers are called "gi"
identifiers. In maintaining GenBank, NCBI generates a new gi if a sequence
has changed, and then creates pointers between the old and new gis. Retrieval
of the particular version of a sequence associated with a gi will always be

3.5.8 KEYWORDS Format

  The KEYWORDS field does not appear in unannotated entries, but is
required in all annotated entries. Keywords are separated by
semicolons; a "keyword" may be a single word or a phrase consisting of
several words. Each line in the keywords field ends in a semicolon;
the last line ends with a period. If no keywords are included in the
entry, the KEYWORDS record contains only a period.

3.5.9 SEGMENT Format

  The SEGMENT keyword is used when two (or more) entries of known
relative orientation are separated by a short (<10 kb) stretch of DNA.
It is limited to one line of the form `n of m', where `n' is the
segment number of the current entry and `m' is the total number of

3.5.10 SOURCE Format

  The SOURCE field consists of two parts. The first part is found after
the SOURCE keyword and contains free-format information including an
abbreviated form of the organism name followed by a molecule type;
multiple lines are allowed, but the last line must end with a period.
The second part consists of information found after the ORGANISM
subkeyword. The formal scientific name for the source organism (genus
and species, where appropriate) is found on the same line as ORGANISM.
The records following the ORGANISM line list the taxonomic
classification levels, separated by semicolons and ending with a

3.5.11 REFERENCE Format

  The REFERENCE field consists of five parts: the keyword REFERENCE, and
the subkeywords AUTHORS, TITLE (optional), JOURNAL, MEDLINE (optional),
and REMARK (optional).

  The REFERENCE line contains the number of the particular reference and
(in parentheses) the range of bases in the sequence entry reported in
this citation. Additional prose notes may also be found within the
parentheses. The numbering of the references does not reflect
publication dates or priorities.

  The AUTHORS line lists the authors in the order in which they appear
in the cited article. Last names are separated from initials by a
comma (no space); there is no comma before the final `and'. The list
of authors ends with a period.  The TITLE line is an optional field,
although it appears in the majority of entries. It does not appear in
unpublished sequence data entries that have been deposited directly
into the GenBank data bank, the EMBL Nucleotide Sequence Data Library,
or the DNA Data Bank of Japan. The TITLE field does not end with a

  The JOURNAL line gives the appropriate literature citation for the
sequence in the entry. The word `Unpublished' will appear after the
JOURNAL subkeyword if the data did not appear in the scientific
literature, but was directly deposited into the data bank. For
published sequences the JOURNAL line gives the Thesis, Journal, or
Book citation, including the year of publication, the specific
citation, or In press.

  The MEDLINE line provides the National Library of Medicine's Medline
unique identifier for a citation (if known). Medline UIs are 8 digit

  The REMARK line is a textual comment that specifies the relevance
of the citation to the entry.

3.5.12 FEATURES Format

  GenBank releases use a feature table format designed jointly by
GenBank, the EMBL Nucleotide Sequence Data Library, and the DNA Data
Bank of Japan. This format is in use by all three databases. The
most complete and accurate Feature Table documentation can be found
on the Web at:

  The Feature Table specification is also available as a printed
document: `The DDBJ/EMBL/GenBank Feature Table: Definition'. Contact
GenBank at the address shown on the first page of these Release Notes
if you would like a copy.

  The feature table contains information about genes and gene products,
as well as regions of biological significance reported in the
sequence. The feature table contains information on regions of the
sequence that code for proteins and RNA molecules. It also enumerates
differences between different reports of the same sequence, and
provides cross-references to other data collections, as described in
more detail below.

  The first line of the feature table is a header that includes the
keyword `FEATURES' and the column header `Location/Qualifier.' Each
feature consists of a descriptor line containing a feature key and a
location (see sections below for details). If the location does not
fit on this line, a continuation line may follow. If further
information about the feature is required, one or more lines
containing feature qualifiers may follow the descriptor line.

  The feature key begins in column 6 and may be no more than 15
characters in length. The location begins in column 22. Feature
qualifiers begin on subsequent lines at column 22. Location,
qualifier, and continuation lines may extend from column 22 to 80.

  Feature tables are required, due to the mandatory presence of the
source feature. The sections below provide a brief introduction to
the feature table format. Feature Key Names

  The first column of the feature descriptor line contains the feature
key. It starts at column 6 and can continue to column 20. The list of
valid feature keys is shown below.

allele		Related strain contains alternative gene form
attenuator	Sequence related to transcription termination
C_region	Span of the C immunological feature
CAAT_signal	`CAAT box' in eukaryotic promoters
CDS		Sequence coding for amino acids in protein (includes
		stop codon)
conflict	Independent sequence determinations differ
D-loop      	Displacement loop
D_segment	Span of the D immunological feature
enhancer	Cis-acting enhancer of promoter function
exon		Region that codes for part of spliced mRNA
GC_signal	`GC box' in eukaryotic promoters
iDNA		Intervening DNA eliminated by recombination
intron		Transcribed region excised by mRNA splicing
J_region	Span of the J immunological feature
LTR		Long terminal repeat
mat_peptide	Mature peptide coding region (does not include stop codon)
misc_binding	Miscellaneous binding site
misc_difference	Miscellaneous difference feature
misc_feature	Region of biological significance that cannot be described
		by any other feature
misc_recomb	Miscellaneous recombination feature
misc_RNA	Miscellaneous transcript feature not defined by other RNA keys
misc_signal	Miscellaneous signal
misc_structure	Miscellaneous DNA or RNA structure
modified_base	The indicated base is a modified nucleotide
mRNA		Messenger RNA
mutation 	A mutation alters the sequence here
N_region	Span of the N immunological feature
old_sequence	Presented sequence revises a previous version
polyA_signal	Signal for cleavage & polyadenylation
polyA_site	Site at which polyadenine is added to mRNA
precursor_RNA	Any RNA species that is not yet the mature RNA product
prim_transcript	Primary (unprocessed) transcript
primer		Primer binding region used with PCR
primer_bind	Non-covalent primer binding site
promoter	A region involved in transcription initiation
protein_bind	Non-covalent protein binding site on DNA or RNA
RBS		Ribosome binding site
rep_origin	Replication origin for duplex DNA
repeat_region	Sequence containing repeated subsequences
repeat_unit	One repeated unit of a repeat_region
rRNA		Ribosomal RNA
S_region	Span of the S immunological feature
satellite	Satellite repeated sequence
scRNA		Small cytoplasmic RNA
sig_peptide	Signal peptide coding region
snRNA		Small nuclear RNA
stem_loop	Hair-pin loop structure in DNA or RNA
STS		Sequence Tagged Site; operationally unique sequence that
		identifies the combination of primer spans used in a PCR assay
TATA_signal	`TATA box' in eukaryotic promoters
terminator	Sequence causing transcription termination
transit_peptide	Transit peptide coding region
transposon	Transposable element (TN)
tRNA 		Transfer RNA
unsure		Authors are unsure about the sequence in this region
V_region	Span of the V immunological feature
variation 	A related population contains stable mutation
- (hyphen)	Placeholder
-10_signal	`Pribnow box' in prokaryotic promoters
-35_signal	`-35 box' in prokaryotic promoters
3'clip		3'-most region of a precursor transcript removed in processing
3'UTR		3' untranslated region (trailer)
5'clip		5'-most region of a precursor transcript removed in processing
5'UTR		5' untranslated region (leader) Feature Location

  The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.

  Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.

Location descriptors can be one of the following:

1. A single base;

2. A contiguous span of bases;

3. A site between two bases;

4. A single base chosen from a range of bases;

5. A single base chosen from among two or more specified bases;

6. A joining of sequence spans;

7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;

8. A literal sequence (a string of bases enclosed in quotation marks).

  A site between two residues, such as an endonuclease cleavage site, is
indicated by listing the two bases separated by a carat (e.g., 23^24).

  A single residue chosen from a range of residues is indicated by the
number of the first and last bases in the range separated by a single
period (e.g., 23.79). The symbols < and > indicate that the end point
of the range is beyond the specified base number.

  A contiguous span of bases is indicated by the number of the first and
last bases in the range separated by two periods (e.g., 23..79). The
symbols < and > indicate that the end point of the range is beyond the
specified base number. Starting and ending positions can be indicated
by base number or by one of the operators described below.

  Operators are prefixes that specify what must be done to the indicated
sequence to locate the feature. The following are the operators
available, along with their most common format and a description.

complement (location): The feature is complementary to the location
indicated. Complementary strands are read 5 to 3.

join (location, location, .. location): The indicated elements should
be placed end to end to form one contiguous sequence.

order (location, location, .. location): The elements are found in the
specified order in the 5 to 3 direction, but nothing is implied about
the rationality of joining them.

group (location, location, .. location): The elements are related and
should be grouped together, but no order is implied.

one-of (location, location, .. location): The element can be any one,
but only one, of the items listed.  Feature Qualifiers

  Qualifiers provide additional information about features. They take
the form of a slash (/) followed by a qualifier name and, if
applicable, an equal sign (=) and a qualifier value. Feature
qualifiers begin at column 22.

Qualifiers convey many types of information. Their values can,
therefore, take several forms:

1. Free text;
2. Controlled vocabulary or enumerated values;
3. Citations or reference numbers;
4. Sequences;
5. Feature labels.

  Text qualifier values must be enclosed in double quotation marks. The
text can consist of any printable characters (ASCII values 32-126
decimal). If the text string includes double quotation marks, each set
must be `escaped' by placing a double quotation mark in front of it
(e.g., /note="This is an example of ""escaped"" quotation marks").

  Some qualifiers require values selected from a limited set of choices.
For example, the `/direction' qualifier has only three values `left,'
`right,' or `both.' These are called controlled vocabulary qualifier
values. Controlled qualifier values are not case sensitive; they can
be entered in any combination of upper- and lowercase without changing
their meaning.

  Citation or published reference numbers for the entry should be
enclosed in square brackets ([]) to distinguish them from other

  A literal sequence of bases (e.g., "atgcatt") should be enclosed in
quotation marks. Literal sequences are distinguished from free text by
context. Qualifiers that take free text as their values do not take
literal sequences, and vice versa.

  The `/label=' qualifier takes a feature label as its qualifier.
Although feature labels are optional, they allow unambiguous
references to the feature. The feature label identifies a feature
within an entry; when combined with the accession number and the name
of the data bank from which it came, it is a unique tag for that
feature. Feature labels must be unique within an entry, but can be the
same as a feature label in another entry. Feature labels are not case
sensitive; they can be entered in any combination of upper-and
lowercase without changing their meaning.

The following is a list of valid feature qualifiers.

/anticodon	Location of the anticodon of tRNA and the amino acid
for which it codes

/bound_moiety	Moiety bound

/citation	Reference to a citation providing the claim of or
evidence for a feature

/codon		Specifies a codon that is different from any found in the
reference genetic code

/codon_start	Indicates the first base of the first complete codon
in a CDS (as 1 or 2 or 3)

/cons_splice	Identifies intron splice sites that do not conform to
the 5'-GT... AG-3' splice site consensus

/db_xref	A database cross-reference; pointer to related information
in another database

/direction	Direction of DNA replication

/EC_number	Enzyme Commission number for the enzyme product of the

/evidence	Value indicating the nature of supporting evidence

/frequency	Frequency of the occurrence of a feature

/function	Function attributed to a sequence

/gene		Symbol of the gene corresponding to a sequence region (usable
with all features)

/label		A label used to permanently identify a feature

/map		Map position of the feature in free-format text

/mod_base	Abbreviation for a modified nucleotide base

/note		Any comment or additional information

/number		A number indicating the order of genetic elements
(e.g., exons or introns) in the 5 to 3 direction

/organism	Name of organism if different from that contained in
the entry's ORGANISM field

/partial	Differentiates between complete regions and partial ones

/phenotype	Phenotype conferred by the feature

/product	Name of a product encoded by the sequence

/pseudo		Indicates that this feature is a non-functional
version of the element named by the feature key

/rpt_family	Type of repeated sequence; Alu or Kpn, for example

/rpt_type	Organization of repeated sequence

/rpt_unit	Identity of repeat unit that constitutes a repeat_region

/standard_name	Accepted standard name for this feature

/transl_except	Translational exception: single codon, the translation
of which does not conform to the reference genetic code

/translation	Amino acid translation of coding region (automatically

/type		Name of a strain if different from that in the SOURCE field

/usedin		Indicates that feature is used in a compound feature
in another entry Cross-Reference Information

  One type of information in the feature table lists cross-references to
the annual compilation of transfer RNA sequences in Nucleic Acids
Research, which has kindly been sent to us on CD-ROM by Dr. Sprinzl.
Each tRNA entry of the feature table contains a /note= qualifier that
includes a reference such as `(NAR: 1234)' to identify code 1234 in
the NAR compilation. When such a cross-reference appears in an entry
that contains a gene coding for a transfer RNA molecule, it refers to
the code in the tRNA gene compilation. Similar cross-references in
entries containing mature transfer RNA sequences refer to the
companion compilation of tRNA sequences published by D.H. Gauss and M.
Sprinzl in Nucleic Acids Research. Feature Table Examples

  In the first example a number of key names, feature locations, and
qualifiers are illustrated, taken from different sequences. The first
table entry is a coding region consisting of a simple span of bases
and including a /gene qualifier. In the second table entry, an NAR
cross-reference is given (see the previous section for a discussion of
these cross-references). The third and fourth table entries use the
symbols `<`and `>' to indicate that the beginning or end of the
feature is beyond the range of the presented sequence. In the fifth
table entry, the symbol `^' indicates that the feature is between

1       10        20        30        40        50        60        70       79
     CDS             5..1261
                     /product="alpha-1-antitrypsin precursor"
     tRNA            1..87
                     /note="Leu-tRNA-CAA (NAR: 1057)"
     mRNA            1..>66
                     /note="alpha-1-acid glycoprotein mRNA"
     transposon      <1..267
                     /note="insertion element IS5"
     misc_recomb     105^106
                     /note="B.subtilis DNA end/IS5 DNA start"
     conflict        258
1       10        20        30        40        50        60        70       79

Example 10. Feature Table Entries

The next example shows the representation for a CDS that spans more
than one entry.

1       10        20        30        40        50        60        70       79
LOCUS       HUMPGAMM1    3688 bp ds-DNA             PRI       15-OCT-1990
DEFINITION  Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M)
            gene, 5' end.
ACCESSION   M55673 M25818 M27095
KEYWORDS    phosphoglycerate mutase.
SEGMENT     1 of 2
FEATURES             Location/Qualifiers
     CAAT_signal     1751..1755
     TATA_signal     1791..1799
     exon            1820..2274
     intron          2275..2377
     exon            2378..2558
LOCUS       HUMPGAMM2     677 bp ds-DNA             PRI       15-OCT-1990
DEFINITION  Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M),
            exon 3.
ACCESSION   M55674 M25818 M27096
KEYWORDS    phosphoglycerate mutase.
SEGMENT     2 of 2
FEATURES             Location/Qualifiers
     exon            255..457
     intron          order(M55673:2559..>3688,<1..254)
     mRNA            join(M55673:1820..2274,M55673:2378..2558,255..457)
     CDS             join(M55673:1861..2274,M55673:2378..2558,255..421)
                     /note="muscle-specific isozyme"
                     /product="phosphoglycerate mutase"
1       10        20        30        40        50        60        70       79

Example 11. Joining Sequences

3.5.13 ORIGIN Format

  The ORIGIN record may be left blank, may appear as `Unreported.' or
may give a local pointer to the sequence start, usually involving an
experimentally determined restriction cleavage site or the genetic
locus (if available). The ORIGIN record ends in a period if it
contains data, but does not include the period if the record is left
empty (in contrast to the KEYWORDS field which contains a period
rather than being left blank).

3.5.14 SEQUENCE Format

  The nucleotide sequence for an entry is found in the records following
the ORIGIN record. The sequence is reported in the 5 to 3 direction.
There are sixty bases per record, listed in groups of ten bases
followed by a blank, starting at position 11 of each record. The
number of the first nucleotide in the record is given in columns 4 to
9 (right justified) of the record.


  NCBI is supplying sequence data in the GenBank flat file format to
maintain compatibility with existing software which require that
particular format.  Although we have made every effort to ensure
that these data are presented in the traditional flat file format,
if you encounter any problems in using these data with software which
is based upon the flat file format, please contact us at:


  The flat file is just one of many possible report formats that can be
generated from the richer representation supported by the ASN.1 form of the
data.  Developers of new software tools should consider using the ASN.1 form
directly to take advantage of those features.  Documentation and a Software
Developer's Toolkit for ASN.1 are available through NCBI.  You may call NCBI
at (301)496-2475, or subscribe to a developers' electronic newsgroup by
sending your name, address, affiliation, and e-mail address to:


  The Software Developer's Toolkit and PostScript documentation for UNIX,
VMS, Ultrix, AIX, MacOS, DOS, and Microsoft Windows systems is available
in a compressed UNIX tar file by anonymous ftp from '',
in the toolbox/ncbi_tools directory. The file is 'ncbi.tar.Z'.


5.1 Incorrect Gene Symbols in Entries and Index

  The /gene qualifier for many GenBank entries contains values other than the
official gene symbol, such as the product or the standard name of the gene. The
gene symbol index (gbgen.idx) is created from the data in the /gene qualifier
and therefore may contain data other than official gene symbols.


  The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH GenBank Sequence Database.  NCBI distributes
GenBank sequence data by anonymous FTP, e-mail servers and other
network services.  For more information, you may contact NCBI at the
e-mail address:  or by phone: 301-496-2475.

6.1 Registered Trademark Notice

  GenBank (R) is a registered trademark of the U.S. Department of Health
and Human Services for the Genetic Sequence Data Bank.

6.2 Citing GenBank

  If you have used GenBank in your research, we would appreciate it if
you would include a reference to GenBank in all publications related
to that research.

  When citing data in GenBank, it is appropriate to give the sequence
name, primary accession number, and the publication in which the
sequence first appeared.  If the data are unpublished, we urge you to
contact the group which submitted the data to GenBank to see if there
is a recent publication or if they have determined any revisions or
extensions of the data.

  It is also appropriate to list a reference for GenBank itself.  The
following publication, which describes the GenBank database, should
be cited:

    Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J.,
    and Ouellette, B.F.F.  GenBank.  Nucl. Acids Res. 26(1):1-7 (1998)

  The following statement is an example of how you may cite GenBank
data.  It cites the sequence, its primary accession number, the group
who determined the sequence, and GenBank.  The numbers in parentheses
refer to the GenBank citation above and to the REFERENCE in the
GenBank sequence entry.

`We scanned the GenBank (1) data bank for sequence similarities and
found one sequence (2), GenBank accession number J01016, which showed
significant similarity...'

  (1) Benson, D.A. et al. Nucl. Acids Res. 26(1):1-7 (1998)
  (2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)

6.3 GenBank Distribution Formats and Media

  Complete flat file releases of the GenBank database are available only via
anonymous ftp from :

  Each release is cumulative, incorporating all previous GenBank data.
No retrieval software is provided. GenBank distribution via CD-ROM
ceased as of GenBank Release 106.0 (April, 1998).

6.4 Other Methods of Accessing GenBank Data

  Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, 3D structure data, complete genomes,
and associated MEDLINE entries. The system is produced by the National
Center for Biotechnology Information (NCBI), and is available only via
the Internet (using the Web-Entrez and Network-Entrez applications).

  Accessing Entrez is easy: if you have a World Wide Web browser, such as
Netscape or Internet-Explorer, simply point your browser to:

  The Web version of Entrez has all the capabilities of the network version,
but with the visual style of the World Wide Web. If you prefer the "look and
feel" of Network-Entrez, you may download Network-Entrez from the NCBI's
FTP server:

Versions are available for PC/Windows, Macintosh and several Unix variants.

  For information about Network-Entrez, Web-Entrez or any other NCBI
services, you may contact NCBI by e-mail to or by
phone at 301-496-2475.

6.5 Request for Corrections and Comments

  We welcome your suggestions for improvements to GenBank. We are
especially interested to learn of errors or inconsistencies in the
data. Please use the GenBank Error/Suggestion Report Form, which is
part of this distribution of GenBank (located in the file gbdat.frm),
to send your suggestions and corrections by electronic mail to: or to the address on the error/suggestion form.
Please be certain to indicate the GenBank release number (e.g.,
Release 108.0) and the primary accession number of the entry to which
your comments apply; it is helpful if you also give the entry name and
the current contents of any data field for which you are recommending
a change.

6.6  Credits and Acknowledgments

Credits -

GenBank Release Coordination	
	Mark Cavanaugh

GenBank Submission Coordination	
	Francis Ouellette

GenBank Annotation Staff
	Kirsty Bates, Medha Bhagwat, Karen Clark, Irene Fang,
	Michael Fetchko, Pamela Jacques, Anthony Jung, Pierre Ledoux,
	Junga Kim, Maureen Madden, Baishali Maskeri, Jenny McDowell,
	Ilene Mizrachi, Lillian Riddick, Leigh Riley, Susan Schafer,
	Jane Weisemann, and Linda Yankie

Data Management and Preparation
	Serge Bazhin, Mark Cavanaugh, Hsiu-Chuan Chen, Jim Ostell,
	Joel Plotkin, Sergei Shavirin, Karl Sirotkin, Vladimir Soussov,
	Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann,

Database Administration
	Cat Lukens, Eugene Yaschenko

Production and User Support
        Dennis Benson, Peter Cooper, Jim Fleshman, Susan Kimball, 
	Renata McCarthy, Scott McGinnis, Monica Romiti, Barbara Rapp, 
	Steven Rosenthal, Rose Marie Woodsmall, David Wheeler 

Project Direction
	David Lipman

Acknowledgments - 

Contractor support for GenBank production and distribution 
has been provided by Management Systems Designers, Inc., 
ComputerCraft Corporation, and The KEVRIC Company, Inc.

6.7 Disclaimer

  The United States Government makes no representations or warranties
regarding the content or accuracy of the information.  The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose and accepts no responsibility for
any consequences of the receipt or use of the information.

  For additional information about GenBank releases, please contact
NCBI by e-mail at, by phone at (301) 496-2475,
or by mail at:

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Support Center