Release Notes For GenBank Release 101

GBREL.TXT          Genetic Sequence Data Bank
                         15 June 1997

               NCBI-GenBank Flat File Release 101.0

                Distribution CD-ROM Release Notes

 1491069 loci, 966993087 bases, from 1491069 reported sequences

  This document describes the data written on GenBank flat file distribution
CD-ROMs. If you have any questions or comments about GenBank, the CD-ROM, or
this document, please contact NCBI via email at info@ncbi.nlm.nih.gov or:

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

==========================================================================
TABLE OF CONTENTS
==========================================================================

1. INTRODUCTION

1.1 Release 101.0
1.2 Cutoff Date
1.3 Important Changes in Release 101.0
1.4 Upcoming Changes
1.5 Request for Direct Submission of Sequence Data
1.6 Organization of This Document

2. ORGANIZATION OF CD-ROM FILES

2.1 CD-ROM Format
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. FILE FORMATS

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
          3.5.5.1 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
          3.5.12.1 Feature Key Names
          3.5.12.2 Feature Location
          3.5.12.3  Feature Qualifiers
          3.5.12.4 Cross-Reference Information
          3.5.12.5 Feature Table Examples
     3.5.13 ORIGIN Format
     3.5.14 SEQUENCE Format

4. ALTERNATE RELEASES

5. KNOWN PROBLEMS OF THE GENBANK DATABASE

5.1 Incorrect Gene Symbols in Entries and Index

6. GENBANK ADMINISTRATION 

6.1 Registered Trademark Notice
6.2 Citing GenBank
6.3 GenBank Distribution Formats and Media
6.4 Other CD-ROM Titles
6.5 Request for Corrections and Comments
6.6 Credits and Acknowledgments
6.7 Disclaimer

==========================================================================

1. INTRODUCTION

1.1 Release 101.0

  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 Data Bank.  NCBI handles
all GenBank direct submission data 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

       E-MAIL:  gb-sub@ncbi.nlm.nih.gov

Updates and changes to existing GenBank records:

       E-MAIL:  update@ncbi.nlm.nih.gov

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

       http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/

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

*****************************************************************************

  Release 101.0 is a release of sequence data by NCBI in the GenBank flat file
format.  It contains a large number of entries produced at the NLM, derived
from scanning the biomedical literature. 

  GenBank contains sequences submitted directly to the database by authors
as well as entries created at NLM derived from scanning the biomedical
literature. Over 325,000 articles per year from 3400 journals are scanned
for sequence data. They are supplemented by journals in plant and veterinary
sciences through a collaboration with the National Agricultural Library.
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
also available by anonymous FTP to 'ncbi.nlm.nih.gov'.

1.2 Cutoff Date

  This full release, 101.0, incorporates data available to the databases as of
June 7, 1997.  For more recent data, users are advised to download the
update files by anonymous FTP to 'ncbi.nlm.nih.gov' 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:  retrieve@ncbi.nlm.nih.gov

1.3 Important Changes in Release 101.0

  Due to the growth in the number of EST sequences, the EST division is now
being split into 13 pieces.

  For the CD-ROM version of this release, the gbaut.idx "index" file has
been arbitrarily split into two pieces because its size exceeds the capacity
of a single disc. The file names of the pieces are gbaut1.idx and gbaut2.idx .

1.4 Upcoming Changes

  Depending on growth rate, the PRI division may be split into 2 pieces
starting with either Release 102.0 or 103.0 .

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 : gb-sub@ncbi.nlm.nih.gov

  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 ncbi.nlm.nih.gov , 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:   ncbi.nlm.nih.gov/

  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: gb-sub@ncbi.nlm.nih.gov.  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: info@ncbi.nlm.nih.gov or 301-496-2475.

1.6 Organization of This Document

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


2. ORGANIZATION OF CD-ROM FILES

2.1 CD-ROM Format

  The GenBank CD-ROM distribution files are available on ISO-9660
compatible CD-ROM. The data are written as ASCII files with variable
length records. Each record corresponds to one line in the data bank;
a carriage return/line feed pair terminate each line.

The data on the CD-ROMs have both uppercase and lowercase characters.

2.2 Files

  The GenBank flat file release consists of thirty-seven files on the
CD-ROM. 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. gbpri.seq 	- Primate sequence entries.
10. gbrod.seq 	- Rodent sequence entries.
11. gbmam.seq 	- Other mammalian sequence entries.
12. gbvrt.seq 	- Other vertebrate sequence entries.
13. gbinv.seq 	- Invertebrate sequence entries.
14. gbpln.seq 	- Plant sequence entries (including fungi and algae).
15. gbbct.seq 	- Bacterial sequence entries.
16. gbrna.seq 	- Structural RNA sequence entries.
17. gbvrl.seq 	- Viral sequence entries.
18. gbphg.seq 	- Phage sequence entries.
19. gbsyn.seq 	- Synthetic and chimeric sequence entries.
20. gbuna.seq 	- Unannotated sequence entries.
21. gbest1.seq  - EST (expressed sequence tag) sequence entries, part 1.
22. gbest2.seq  - EST (expressed sequence tag) sequence entries, part 2.
23. gbest3.seq  - EST (expressed sequence tag) sequence entries, part 3.
24. gbest4.seq  - EST (expressed sequence tag) sequence entries, part 4.
25. gbest5.seq  - EST (expressed sequence tag) sequence entries, part 5.
26. gbest6.seq  - EST (expressed sequence tag) sequence entries, part 6.
27. gbest7.seq  - EST (expressed sequence tag) sequence entries, part 7.
28. gbest8.seq  - EST (expressed sequence tag) sequence entries, part 8.
29. gbest9.seq  - EST (expressed sequence tag) sequence entries, part 9.
30. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
31. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
32. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
33. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
34. gbpat.seq   - Patent sequence entries.
35. gbsts.seq   - STS (sequence tagged site) sequence entries.
36. gbgss.seq   - GSS (genome survey sequence) sequence entries.
37. 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

 53733924      gbacc.idx
742041603      gbaut.idx
203740315      gbbct.seq
    22899      gbdat.frm
200158454      gbest1.seq
234861217      gbest2.seq
237624347      gbest3.seq
239599609      gbest4.seq
224409410      gbest5.seq
252841947      gbest6.seq
241613860      gbest7.seq
240409454      gbest8.seq
244349910      gbest9.seq
258357676      gbest10.seq
251916277      gbest11.seq
230982874      gbest12.seq
188533620      gbest13.seq
  5654150      gbgen.idx
 61960995      gbgss.seq
 53415172      gbhtg.seq
194808437      gbinv.seq
 62682775      gbjou.idx
 48818271      gbkey.idx
 35811139      gbmam.seq
 77419472      gbpat.seq
  5842433      gbphg.seq
193131487      gbpln.seq
278098301      gbpri.seq
    12926      gbrel.txt
  9370937      gbrna.seq
122986015      gbrod.seq
119287354      gbsdr.txt
126425753      gbsts.seq
 11590667      gbsyn.seq
  6645140      gbuna.seq
138549353      gbvrl.seq
 48572645      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            34836      80550462
EST1           82012      27960235
EST2           82000      30980337
EST3           82002      29761291
EST4           82000      30462872
EST5           82001      29717564
EST6           82000      30343268
EST7           82000      31239249
EST8           82000      32718362
EST9           82000      31557472
EST10          82000      28257071
EST11          82000      27183759
EST12          82000      30639401
EST13          79034      27102113
GSS            25583      14399425
HTG              513      40949369
INV            27363      95938006
MAM            11469      11452910
PAT            62100      20925881
PHG             1293       2021900
PLN            41329      77331725
PRI            71906     109888832
RNA             4815       2494900
ROD            35344      41975793
STS            49199      16900458
SYN             2477       5314564
UNA             2414       2101662
VRL            41785      41395250
VRT            15594      15428956

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 101.0 (chloroplast and mitochon-
drial sequences not included):

Entries      Bases   Species

858696   418051738   Homo sapiens
211426    98380230   Mus musculus
33215     81600223   Caenorhabditis elegans
10379     28389991   Saccharomyces cerevisiae
38713     25255708   Arabidopsis thaliana
21240     23018762   Drosophila melanogaster
4582      17087994   Escherichia coli
9988      12965422   Rattus norvegicus
17509      7693442   Human immunodeficiency virus type 1
14325      5841200   Oryza sativa
4077       4755692   Gallus gallus
979        4164049   Bacillus subtilis
1038       3992657   Schizosaccharomyces pombe
420        3972051   Mycobacterium tuberculosis
144        3829881   Synechocystis sp.
4276       3789342   Bos taurus
6443       3645227   Fugu rubripes
8967       3288874   Brugia malayi
8434       3044892   Toxoplasma gondii
1945       2942222   Xenopus laevis

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

3. FILE FORMATS

  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 thirty-seven files on the distribution CD-ROM 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,
OTHER VERTEBRATE, INVERTEBRATE, PLANT, BACTERIAL, STRUCTURAL RNA, VIRAL,
PHAGE, SYNTHETIC, UNANNOTATED, EXPRESSED SEQUENCE TAG, PATENT, or
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
ZZZZZZZZZZ
 
                    INVERTEBRATE

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
divisions:

 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.

3.3.1 Accession Number Index File

  Accession numbers consist of a single letter followed by five digits.
They provide an unchanging designation for the data with which they
are associated, and we encourage you to cite accession numbers
whenever you refer to data from the data bank. The primary accession
number is the first accession number of an entry. It is unique to that
entry. Citation of that number will enable other investigators to
locate the data no matter what entry name changes or other data bank
reorganizations may occur. The accession numbers, however, carry no
intrinsic information about the data.

  In addition to the primary accession number, some entries have
secondary accession numbers. Secondary accession numbers arise for a
number of reasons. For example, a single accession number may
initially be assigned to the sequence in an article. If it is later
discovered that the sequence must be entered into the data bank as
multiple entries, each entry would receive a new primary accession
number; the previous accession number would appear as the secondary
accession number in each entry.

  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.

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
---------+---------+---------+---------+---------+---------+---------+---------
DNA HELICASE
             ECOHELIV   BCT J04726 ECOUVRD    BCT X00738 FPLTRAX    BCT M38047
             HS2ULL     VRL D10470 HSECOMGEN  VRL M86664 PT4DDA     PHG M93048
             SYNPMMB190 SYN M37846 YSPRHP3    PLN X64583
DNA HELICASE I
             ECOPTRAI5  BCT X57430
DNA HELICASE II
             ECOUVRD2   BCT D00069 HEAMUTB1A  BCT M99049
DNA INVERSION SYSTEM
             ECOP15BG   BCT X62121
DNA INVERTASE
             ECOPIN     BCT K00676 ECOPIN1    BCT X01805 PMUGINMOM  PHG V01463
             STABINR3   BCT X16298 STAINVSA   BCT M36694
DNA J HEATSHOCK PROTEIN
             MSGDNAJHSP BCT M95576
DNA LIGASE
             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
below:

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
JACKSON,D.I.
             RATLCAG1   ROD M18349 RATLCAG2   ROD M18348 RATLCAG3   ROD M18347
             RATLCAI    ROD M25820 RATLCAII   ROD M25821 RATLCAIII  ROD M25822
             RATLCAIV   ROD M25823 RATLCAR    ROD Y00065
JACKSON,F.R.
             DRO16883C  INV X62939 DRO1688ED  INV X62938 DRO1688EP  INV X62937
             DROPER     INV M11969 DROPES     INV X03636 MUSPER     ROD M12039
             MUSURFPER  ROD X02966
JACKSON,I.J.
             MUSHOMA    ROD X03033 MUSNEORP8R ROD X54812 MUSP7H2    ROD X54811
             MUSRPT     ROD M69041 MUSSOFI    ROD X63350 MUSTRP15   ROD X59513
             MUSTYRP2   ROD X63349
JACKSON,I.M.
             RATTRH     ROD M12138
JACKSON,J.
             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
---------+---------+---------+---------+---------+---------+---------+---------
(IN) THE IMMUNE SYSTEM:  132-138, S. KARGER, NEW YORK (1981)
             HUMIGHVX   PRI M35415
(IN) THE LENS: TRANSPARANCY AND CATARACT:  171-179, EURAGE, RIJSWIJK (1986)
             RANCRYG2A  VRT K02264 RANCRYG4A  VRT K02266 RANCRYG5A  VRT M22529
             RANCRYG6A  VRT M22530 RANCRYR    VRT X00659
(IN) THIOREDOXIN AND GLUTAREDOXIN SYSTEMS: STRUCTURE AND FUNCTION: 11-19, UNKNOW
             ECOTRXA1   BCT M54881
(IN) UCLA SYMP. MOL. CELL. BIOL. NEW SER., VOL. 77:  339-352, ALAN R. LISS, INC.
             BOVTRNB2A  MAM M36431 HUMTRNB    PRI M36429 HUMTRNB1   PRI M36430
(IN) UCLA SYMPOSIA:  575-584, ALAN R. LISS, INC., NEW YORK (1987)
             PFAHGPRT   INV M54896
(IN) VIRUS RESEARCH. PROCEEDINGS OF 1973 ICN-UCLA SYMPOSIUM:  533-544, ACADEMIC
             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 'Gene.locus'
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
---------+---------+---------+---------+---------+---------+---------+---------
SUPPRESSOR OF SABLE
             DROSUSG    INV M57889
SUPPRESSOR TWO OF ZESTE
             DROS2ZSTG  INV X56798
SUPRESSOR TWO OF ZESTE
             DROS2ZSTM  INV X56799
SUR
             CHKSRVCNTK VRT M57290
SURC
             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:  gb-sub@ncbi.nlm.nih.gov

  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:  update@ncbi.nlm.nih.gov


3.5 Sequence Entry Files

  The distribution CD-ROM contains fifteen 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
contain:

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 3.5.12.1 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
al.

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.
ACCESSION   K03160
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.
ACCESSION   M34766
KEYWORDS    5S ribosomal RNA.
SOURCE      Acetobacter sp. (strain MB 58) rRNA.
  ORGANISM  Acetobacter sp.
            Prokaryotae; Gracilicutes; Scotobacteria; Aerobic rods and cocci;
            Azotobacteraceae.
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
            sequencing
  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
ORIGIN      
        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.

3.5.5.1 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 2.13.2.4}, {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 identifiers (accession
numbers: first character a letter, the remainder digits). The primary
(first) accession number occupies positions 13 to 18; subsequent
accession numbers occupy positions 20 to 25, 27 to 32, 34 to 39, 41 to
46, 48 to 53, 55 to 60, 62 to 67, and 69 to 74. No punctuation occurs
between accession numbers or after the final accession number;
accession numbers are separated only by one space.

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
possible.

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
segments.

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
period.

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
period.

  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
numbers.

  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 http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/collab/FT/index.html  .

  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.

3.5.12.1 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)
cellular	Region of cellular DNA
conflict	Independent determinations differ
D-loop      	Displacement loop
D_region	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
insertion_seq	Insertion sequence (IS), a small transposon
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
provirus	Proviral sequence
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
virion		Virion (encapsidated) viral sequence
- (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)


3.5.12.2 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.

3.5.12.3  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
numbers.

  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
sequence

/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
generated)

/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

3.5.12.4 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.

3.5.12.5 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
bases.

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
     CDS             5..1261
                     /product="alpha-1-antitrypsin precursor"
                     /map="14q32.1"
                     /gene="PI"
     tRNA            1..87
                     /note="Leu-tRNA-CAA (NAR: 1057)"
                     /anticodon=(pos:35..37,aa:Leu)
     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
                     /replace="t"
                     /citation=[2]
---------+---------+---------+---------+---------+---------+---------+---------
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
                     /gene="PGAM-M"
     TATA_signal     1791..1799
                     /gene="PGAM-M"
     exon            1820..2274
                     /number=1
                     /EC_number="5.4.2.1"
                     /gene="PGAM-M"
     intron          2275..2377
                     /number=1
                     /gene="PGAM2"
     exon            2378..2558
                     /number=2
                     /gene="PGAM-M"
  .
  .
  .
//
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
                     /number=3
                     /gene="PGAM-M"
     intron          order(M55673:2559..>3688,<1..254)
                     /number=2
                     /gene="PGAM-M"
     mRNA            join(M55673:1820..2274,M55673:2378..2558,255..457)
                     /gene="PGAM-M"
     CDS             join(M55673:1861..2274,M55673:2378..2558,255..421)
                     /note="muscle-specific isozyme"
                     /gene="PGAM2"
                     /product="phosphoglycerate mutase"
                     /codon_start=1
                     /translation="MATHRLVMVRHGESTWNQENRFCGWFDAELSEKGTEEAKRGAKA
                     IKDAKMEFDICYTSVLKRAIRTLWAILDGTDQMWLPVVRTWRLNERHYGGLTGLNKAE
                     TAAKHGEEQVKIWRRSFDIPPPPMDEKHPYYNSISKERRYAGLKPGELPTCESLKDTI
                     ARALPFWNEEIVPQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLPTGIPIVY
                     ELNKELKPTKPMQFLGDEETVRKAMEAVAAQGKAK"
  .
  .
  .
//
---------+---------+---------+---------+---------+---------+---------+---------
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.


4. ALTERNATE RELEASES

  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:

              info@ncbi.nlm.nih.gov

  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:

              bits-request@ncbi.nlm.nih.gov

  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 'ncbi.nlm.nih.gov',
in the toolbox/ncbi_tools directory. The file is 'ncbi.tar.Z'.


5. KNOWN PROBLEMS OF THE GENBANK DATABASE

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.


6. GENBANK ADMINISTRATION 

  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 CD-ROM, anonymous FTP, e-mail servers and other
network services.  For more information, you may contact NCBI at the
e-mail address:  info@ncbi.nlm.nih.gov  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., and Ostell, J.
        GenBank.  Nucl. Acids Res. 25(1):1-6 (1997)

  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. 25(1):1-6 (1997)
  (2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)

6.3 GenBank Distribution Formats and Media

  GenBank data are available on industry-standard ISO-9660 CD-ROM.
The standard flat file format is included.  

  This documentation accompanies the nine CD-ROM set entitled
'GenBank (Flat File Format).'  Each release is cumulative, incorporating
all previous GenBank data.  No retrieval software is provided.

6.4 Other CD-ROM Titles

The Entrez CDROM release has been discontined, effective August 15, 1996.

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

The CD-ROM version was discontinued due to the continuing rapid growth
in size of GenBank and other sequence databases, causing the CD-ROM
release to become increasingly unwieldy and inconvenient. The CD-ROM
version also lagged far behind the two Internet versions, Network
Entrez and Web Entrez, in the number of MEDLINE citations available and
in the addition of new databases, including the Genomes division and
the Structure division, as well as links to an increasing number of
on-line journals.  In addition, the two on-line versions of Entrez are
updated daily, compared to the bimonthly CD-ROM updates.

Access to the Internet versions of Entrez is easy.  If you have a World
Wide Web browser, such as Netscape or Explorer, simply point your browser
to http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/.  The Web version of Entrez has all the
capabilities of the CD-ROM version, but with the visual style of the
World Wide Web.  If you preferred the "look and feel" of the CD-ROM
version, you may download Network Entrez from the NCBI's anonymous FTP
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Macintosh and several Unix workstations.

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

Ordering Information

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6.6  Credits and Acknowledgments

Credits -

CD-ROM Data Coordination	
	Mark Cavanaugh

GenBank Submission Coordination	
	Francis Ouellette

GenBank Annotation Staff
	Kirsty Bates, Irene Fang, Michael Fetchko, Junga Kim, 
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Production and User Support
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Graphics
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Project Direction
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Acknowledgments - 

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