NCBI Pongo pygmaeus Annotation Release GCF_028885625.1-RS_2023_04
The genome sequence records for Pongo pygmaeus RefSeq assembly GCF_028885625.1 (NHGRI_mPonPyg2-v1.1-hic.freeze_pri) 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_028885625.1-RS_2023_04 is an update of GCF_028885625.1-RS_2023_03. The known RefSeq transcripts (with NM_ and NR_ prefixes) that were current on Apr 6 2023 were placed on the genome and used to update the annotated features. In addition, model RefSeq predicted in the last full annotation (GCF_028885625.1-RS_2023_03) that were still current on Apr 6 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 GCF_028885625.1-RS_2023_03.
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_028885625.1-RS_2023_04".Date of Entrez queries for transcripts and proteins: Apr 6 2023
Date of submission of annotation to the public databases: Apr 11 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 |
|---|---|---|---|---|---|
| NHGRI_mPonPyg2-v1.1-hic.freeze_pri | GCF_028885625.1 | National Human Genome Research Institute, National Institutes of Health | 02-28-2023 | Reference | 25 assembled chromosomes; unplaced scaffolds |
Gene and feature statistics
Counts and length of annotated features are provided below for each assembly.Feature counts
| Feature | NHGRI_mPonPyg2-v1.1-hic.freeze_pri |
|---|---|
Genes and pseudogenes  | 39,296 |
| protein-coding | 22,044 |
| non-coding | 9,608 |
| Transcribed pseudogenes | 30 |
| Non-transcribed pseudogenes | 7,345 |
| genes with variants | 13,104 |
| Immunoglobulin/T-cell receptor gene segments | 224 |
| other | 45 |
| mRNAs | 68,930 |
| fully-supported | 67,885 |
| with > 5% ab initio | 614 |
| partial | 89 |
| with filled gap(s) | 0 |
| known RefSeq (NM_) | 0 |
| model RefSeq (XM_) | 68,930 |
| non-coding RNAs | 13,458 |
| fully-supported | 7,108 |
| with > 5% ab initio | 0 |
| partial | 2 |
| with filled gap(s) | 0 |
| known RefSeq (NR_) | 0 |
| model RefSeq (XR_) | 13,006 |
| pseudo transcripts | 30 |
| fully-supported | 23 |
| with > 5% ab initio | 0 |
| partial | 0 |
| with filled gap(s) | 0 |
| known RefSeq (NR_) | 0 |
| model RefSeq (XR_) | 30 |
| CDSs | 69,154 |
| fully-supported | 67,885 |
| with > 5% ab initio | 707 |
| partial | 92 |
| with major correction(s) | 909 |
| known RefSeq (NP_) | 0 |
| model RefSeq (XP_) | 68,930 |
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 | 31,697 | 42,933 | 11,336 | 43 | 2,493,839 |
| All transcripts | 82,388 | 3,433 | 2,814 | 43 | 108,259 |
| mRNA | 68,930 | 3,760 | 3,109 | 66 | 108,259 |
| misc_RNA | 2,886 | 3,171 | 2,624 | 118 | 19,723 |
| tRNA | 452 | 74 | 73 | 71 | 93 |
| lncRNA | 4,224 | 1,802 | 1,161 | 99 | 26,250 |
| snoRNA | 1,179 | 111 | 104 | 43 | 330 |
| snRNA | 1,586 | 110 | 107 | 59 | 200 |
| rRNA | 3,086 | 2,143 | 1,871 | 119 | 5,112 |
| Single-exon transcripts | 2,140 | 1,491 | 959 | 66 | 15,765 |
| coding transcripts (NM_/XM_ ) | 2,139 | 1,492 | 958 | 66 | 15,765 |
| non-coding transcripts (NR_/XR_ ) | 1 | 1,053 | 1,053 | 1,053 | 1,053 |
| CDSs | 68,930 | 1,926 | 1,476 | 63 | 107,034 |
| Exons | 287,510 | 372 | 141 | 1 | 35,245 |
| in coding transcripts (NM_/XM_ ) | 269,265 | 363 | 140 | 1 | 35,245 |
| in non-coding transcripts (NR_/XR_ ) | 31,268 | 367 | 142 | 2 | 20,376 |
| Introns | 250,873 | 7,052 | 1,725 | 30 | 1,035,957 |
| in coding transcripts (NM_/XM_ ) | 237,770 | 6,951 | 1,706 | 30 | 1,035,957 |
| in non-coding transcripts (NR_/XR_ ) | 25,925 | 7,073 | 1,835 | 30 | 551,514 |
Transcripts per gene, exons per transcript
| Mean | Median | Min | Max | |
|---|---|---|---|---|
| Number of transcripts per gene | 2.62 | 1 | 1 | 50 |
| Number of exons per transcript | 11.24 | 9 | 1 | 361 |
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 primates_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