NCBI Orycteropus afer afer Annotation Release 100
The RefSeq genome records for Orycteropus afer afer were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.
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
- Masking of genomic sequence: How much of the genome was masked
- Transcript and protein alignments: The number and type of evidence retrieved from public databases and used for gene prediction
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 NCBI Orycteropus afer afer Annotation Release 100Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: May 9 2014
Date of submission of annotation to the public databases: May 14 2014
Software version: 6.0
Assemblies
The following assemblies were included in this annotation run:| Assembly name | Assembly accession | Submitter | Assembly date | Reference/Alternate | Assembly content |
|---|---|---|---|---|---|
| OryAfe1.0 | GCF_000298275.1 | Broad Institute | 09-20-2012 | Reference | 1 assembled chromosomes; unplaced scaffolds |
Gene and feature statistics
Counts and length of annotated features are provided below for each assembly.Feature counts
| Feature | OryAfe1.0 |
|---|---|
Genes and pseudogenes  | 22,573 |
| protein-coding | 19,607 |
| non-coding | 54 |
| pseudogenes | 2,912 |
| genes with variants | 3,372 |
| mRNAs | 25,531 |
| fully-supported | 18,329 |
| with > 5% ab initio | 3,093 |
| partial | 537 |
| with filled gap(s) | 0 |
| known RefSeq (NM_) | 0 |
| model RefSeq (XM_) | 25,531 |
| Other RNAs | 618 |
| fully-supported | 13 |
| with > 5% ab initio | 0 |
| partial | 0 |
| with filled gap(s) | 0 |
| known RefSeq (NR_) | 0 |
| model RefSeq (XR_) | 13 |
| CDSs | 25,640 |
| fully-supported | 18,329 |
| with > 5% ab initio | 3,291 |
| partial | 561 |
| with major correction(s) | 1,150 |
| known RefSeq (NP_) | 0 |
| model RefSeq (XP_) | 25,531 |
Detailed reports
Feature lengths
| Feature | Count | Mean length (bp) | Median length (bp) | Min length (bp) | Max length (bp) |
|---|---|---|---|---|---|
| Genes | 19,661 | 66,828 | 18,282 | 71 | 2,295,160 |
| All transcripts | 26,149 | 1,939 | 1,482 | 70 | 107,502 |
| mRNA | 25,531 | 1,984 | 1,512 | 75 | 107,502 |
| misc_RNA | 7 | 3,438 | 2,742 | 1,112 | 9,905 |
| tRNA | 605 | 74 | 73 | 70 | 86 |
| lncRNA | 6 | 353 | 379 | 276 | 399 |
| Single-exon transcripts | 2,402 | 1,032 | 942 | 85 | 6,840 |
| coding transcripts (NM_/XM_ ) | 2,402 | 1,032 | 942 | 85 | 6,840 |
| CDSs | 25,531 | 1,730 | 1,305 | 75 | 106,266 |
| Exons | 197,589 | 196 | 129 | 1 | 17,106 |
| in coding transcripts (NM_/XM_ ) | 197,552 | 196 | 129 | 1 | 17,106 |
| in non-coding transcripts (NR_/XR_ ) | 159 | 163 | 128 | 4 | 1,136 |
| Introns | 176,043 | 7,909 | 1,550 | 30 | 1,155,757 |
| in coding transcripts (NM_/XM_ ) | 176,021 | 7,909 | 1,550 | 30 | 1,155,757 |
| in non-coding transcripts (NR_/XR_ ) | 146 | 12,950 | 3,031 | 80 | 167,557 |
Transcripts per gene, exons per transcript
| Mean | Median | Min | Max | |
|---|---|---|---|---|
| Number of transcripts per gene | 1.31 | 1 | 1 | 28 |
| Number of exons per transcript | 10.57 | 8 | 1 | 349 |
Masking of genomic sequence
Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker for each assembly. RepeatMasker results are only used for organisms for which a comprehensive repeat library is available.
For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.| Assembly name | Assembly accession | % Masked with RepeatMasker | % Masked with WindowMasker |
|---|---|---|---|
| OryAfe1.0 | GCF_000298275.1 | 24.41% | 38.66% |
Transcript and protein alignments
The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign or ProSplign and passed to Gnomon, NCBI's gene prediction software.
Depending on the other evidence available, long 454 reads (with average length above 250 nt) may be aligned as traditional evidence and reported in the Transcript alignments section or aligned with short reads and reported in the Short read transcript alignments section.
Transcript alignments
Short read transcript alignments
No short read transcripts were used in this annotationProtein alignments
| Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by ProSplign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
|---|---|---|---|---|---|
| Afrotheria GenBank | 74 | 62 (83.78%) | 62 (83.78%) | 78.14% | 90.05% |
Afrotheria known RefSeq (NP_) | 49 | 45 (91.84%) | 45 (91.84%) | 77.55% | 89.70% |
| Cetartiodactyla GenBank | 29,061 | 27,960 (96.21%) | 27,960 (96.21%) | 74.16% | 83.53% |
Cetartiodactyla known RefSeq (NP_) | 18,653 | 18,330 (98.27%) | 18,330 (98.27%) | 76.88% | 83.23% |
| Homo sapiens GenBank | 124,926 | 111,823 (89.51%) | 111,823 (89.51%) | 75.81% | 80.70% |
Homo sapiens known RefSeq (NP_) | 37,246 | 35,900 (96.39%) | 35,900 (96.39%) | 76.64% | 80.24% |
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
- 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