NCBI Mus musculus Annotation Release GCF_000001635.27-RS_2023_04

The genome sequence records for Mus musculus RefSeq assembly GCF_000001635.27 (GRCm39) were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies.

Annotation Release GCF_000001635.27-RS_2023_04 is an update of NCBI Mus musculus Annotation Release 109. The known RefSeq transcripts (with NM_ and NR_ prefixes) that were current on Apr 5 2023 were placed on the genome and used to update the annotated features. In addition, model RefSeq predicted in the last full annotation (NCBI Mus musculus Annotation Release 109) that were still current on Apr 5 2023 were included in the updated annotation. These models were not re-calculated for this update. For more information on the evidence used for generating the model RefSeq, please consult the report for NCBI Mus musculus Annotation Release 109.

The annotation products are available in the sequence databases and on the FTP site.

This report provides:

Annotation Release information: The name of the release, important dates, the software version
Assemblies: A brief description of the annotated assembly(ies)
Gene and feature statistics: The counts and characteristics of the annotated features
BUSCO results: Annotation completeness assessed with BUSCO

For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.

Annotation Release information

This annotation should be referred to as "GCF_000001635.27-RS_2023_04".

Date of Entrez queries for transcripts and proteins: Apr 5 2023
Date of submission of annotation to the public databases: Apr 10 2023
Software version: 10.1

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
GRCm39	GCF_000001635.27	Genome Reference Consortium	06-24-2020	Reference	22 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

Counts and length of annotated features are provided below for each assembly.

Feature counts

Feature	GRCm39
Genes and pseudogenes	50,562
protein-coding	22,192
non-coding	17,463
Transcribed pseudogenes	511
Non-transcribed pseudogenes	9,841
genes with variants	18,493
Immunoglobulin/T-cell receptor gene segments	490
other	65
mRNAs	96,179
fully-supported	95,899
with > 5% ab initio	112
partial	58
with filled gap(s)	0
known RefSeq (NM_)	46,222
model RefSeq (XM_)	49,957
non-coding RNAs	39,257
fully-supported	35,678
with > 5% ab initio	0
partial	4
with filled gap(s)	0
known RefSeq (NR_)	8,888
model RefSeq (XR_)	29,051
pseudo transcripts	582
fully-supported	573
with > 5% ab initio	0
partial	0
with filled gap(s)	0
known RefSeq (NR_)	511
model RefSeq (XR_)	71
CDSs	96,682
fully-supported	95,899
with > 5% ab initio	155
partial	56
with major correction(s)	32
known RefSeq (NP_)	46,235
model RefSeq (XP_)	49,957

Detailed reports

The counts below do not include pseudogenes.

Feature lengths

Feature	Count	Mean length (bp)	Median length (bp)	Min length (bp)	Max length (bp)
Genes	39,720	33,179	10,318	10	3,171,119
All transcripts	135,436	3,837	2,906	15	148,183
mRNA	96,179	4,248	3,360	111	141,950
misc_RNA	10,758	4,236	3,401	120	148,183
miRNA	2,110	22	22	15	27
tRNA	422	73	72	59	87
lncRNA	23,512	2,771	1,414	36	141,249
snoRNA	1,330	118	130	28	320
snRNA	1,000	115	107	59	332
antisense_RNA	9	2,648	2,487	865	5,023
rRNA	64	157	121	119	1,582
telomerase_RNA	1	397	397	397	397
RNase_MRP_RNA	1	275	275	275	275
RNase_P_RNA	4	259	238	235	325
Y_RNA	2	106	111	101	111
scRNA	3	219	299	58	299
Single-exon transcripts	2,929	1,560	951	111	99,852
coding transcripts (NM_/XM_ )	2,692	1,399	948	111	99,852
non-coding transcripts (NR_/XR_ )	237	3,383	2,152	147	83,437
CDSs	96,192	2,061	1,473	78	106,392
Exons	351,581	484	151	1	139,958
in coding transcripts (NM_/XM_ )	284,947	422	145	1	139,958
in non-coding transcripts (NR_/XR_ )	123,281	523	152	2	112,051
Introns	294,594	6,512	1,570	26	1,067,346
in coding transcripts (NM_/XM_ )	246,383	6,492	1,525	26	1,067,346
in non-coding transcripts (NR_/XR_ )	102,675	5,517	1,535	30	601,637

Transcripts per gene, exons per transcript

	Mean	Median	Min	Max
Number of transcripts per gene	3.42	1	1	96
Number of exons per transcript	11.64	8	1	349

BUSCO analysis of gene annotation

BUSCO v4.1.4 was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the glires_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation.

References

RefSeq: Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, Dicuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Nucleic Acids Research 2014, 42(Database issue):D756-63
BUSCO: Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. Molecular biology and evolution 2021.38(10):4647-4654
RepeatMasker: Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2004. http://www.repeatmasker.org
WindowMasker: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. Bioinformatics 2006, 2:134-41
Splign: Kapustin Y, Souvorov A, Tatusova T, Lipman D. Biology Direct 2008, 3:20
STAR: Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. Bioinformatics 2013 Jan 1;29(1):15-21.
Minimap2: Li H. Bioinformatics 2018 Sep 15;34(18):3094-3100

RefSeq

Integrated reference sequences