NCBI Rattus norvegicus Annotation Release 104
The RefSeq genome records for Rattus norvegicus 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
- Similarity of alternate and reference assemblies: The similarity of the alternate assemblies to the reference
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 Rattus norvegicus Annotation Release 104Annotation release ID: 104
Date of Entrez queries for transcripts and proteins: Nov 22 2013
Date of submission of annotation to the public databases: Dec 9 2013
Software version: 5.2
Assemblies
The following assemblies were included in this annotation run:| Assembly name | Assembly accession | Submitter | Assembly date | Reference/Alternate | Assembly content |
|---|---|---|---|---|---|
| Rnor_5.0 | GCF_000001895.4 | Rat Genome Sequencing Consortium | 03-16-2012 | Reference | 22 assembled chromosomes; unplaced scaffolds |
| Rn_Celera | GCF_000002265.2 | Celera Genomics | 12-06-2006 | Alternate | 21 assembled chromosomes; unplaced scaffolds |
Gene and feature statistics
Counts and length of annotated features are provided below for each assembly.Feature counts
| Feature | Rnor_5.0 | Rn_Celera |
|---|---|---|
Genes and pseudogenes  | 37,726 | 35,498 |
| protein-coding | 23,374 | 22,027 |
| non-coding | 8,077 | 7,581 |
| pseudogenes | 6,275 | 5,890 |
| mRNAs | 50,774 | 26,950 |
| fully-supported | 49,508 | 26,077 |
| with > 5% ab initio | 611 | 422 |
| partial | 2,304 | 1,833 |
| known RefSeq (NM_) | 17,333 | 17,228 |
| model RefSeq (XM_) | 33,441 | 9,722 |
| model RefSeq (XM_) with correction | 367 | 342 |
| Other RNAs | 13,971 | 12,529 |
| fully-supported | 13,306 | 11,858 |
| with > 5% ab initio | 0 | 0 |
| partial | 4 | 7 |
| known RefSeq (NR_) | 459 | 449 |
| model RefSeq (XR_) | 12,863 | 11,421 |
| CDSs | 51,268 | 27,352 |
| fully-supported | 49,508 | 26,077 |
| with > 5% ab initio | 746 | 515 |
| partial | 1,851 | 1,371 |
| known RefSeq (NP_) | 17,331 | 17,225 |
| model RefSeq (XP_) | 33,441 | 9,722 |
| model RefSeq (XP_) with correction | 367 | 342 |
Detailed reports
Feature lengths
| Feature | Count | Mean length (bp) | Median length (bp) | Min length (bp) | Max length (bp) |
|---|---|---|---|---|---|
| Genes | 31,451 | 33,153 | 10,894 | 59 | 2,224,084 |
| All transcripts | 64,745 | 2,820 | 2,204 | 17 | 103,298 |
| mRNA | 50,774 | 3,093 | 2,460 | 121 | 103,298 |
| misc_RNA | 1,559 | 3,071 | 2,465 | 97 | 15,461 |
| miRNA | 685 | 22 | 22 | 17 | 25 |
| tRNA | 352 | 73 | 72 | 69 | 86 |
| lncRNA | 11,367 | 1,821 | 1,249 | 33 | 31,625 |
| snRNA | 1 | 60 | 60 | 60 | 60 |
| rRNA | 5 | 3,117 | 1,874 | 120 | 8,647 |
| telomerase_RNA | 1 | 388 | 388 | 388 | 388 |
| RNase_MRP_RNA | 1 | 257 | 257 | 257 | 257 |
| Single-exon transcripts | 3,236 | 1,165 | 942 | 121 | 9,707 |
| coding transcripts (NM_/XM_ ) | 3,217 | 1,165 | 942 | 121 | 9,707 |
| non-coding transcripts (NR_/XR_ ) | 19 | 1,024 | 502 | 152 | 4,485 |
| CDSs | 50,774 | 1,841 | 1,350 | 66 | 102,066 |
| Exons | 281,146 | 330 | 141 | 1 | 24,129 |
| in coding transcripts (NM_/XM_ ) | 248,723 | 306 | 138 | 1 | 24,129 |
| in non-coding transcripts (NR_/XR_ ) | 39,231 | 457 | 165 | 1 | 16,529 |
| Introns | 235,956 | 5,185 | 1,404 | 25 | 1,095,654 |
| in coding transcripts (NM_/XM_ ) | 212,435 | 5,209 | 1,390 | 25 | 1,095,654 |
| in non-coding transcripts (NR_/XR_ ) | 30,189 | 4,715 | 1,451 | 30 | 597,081 |
Transcripts per gene, exons per transcript
| Mean | Median | Min | Max | |
|---|---|---|---|---|
| Number of transcripts per gene | 2.06 | 1 | 1 | 39 |
| Number of exons per transcript | 9.87 | 7 | 1 | 319 |
| Feature | Count | Mean length (bp) | Median length (bp) | Min length (bp) | Max length (bp) |
|---|---|---|---|---|---|
| Genes | 29,608 | 33,548 | 10,754 | 59 | 2,188,624 |
| All transcripts | 39,479 | 2,473 | 1,819 | 17 | 107,828 |
| mRNA | 26,950 | 2,784 | 2,088 | 128 | 107,828 |
| misc_RNA | 773 | 3,134 | 2,408 | 51 | 14,278 |
| miRNA | 680 | 22 | 22 | 17 | 25 |
| tRNA | 364 | 74 | 73 | 69 | 86 |
| lncRNA | 10,708 | 1,880 | 1,276 | 33 | 19,772 |
| snRNA | 1 | 60 | 60 | 60 | 60 |
| rRNA | 1 | 120 | 120 | 120 | 120 |
| telomerase_RNA | 1 | 388 | 388 | 388 | 388 |
| RNase_MRP_RNA | 1 | 257 | 257 | 257 | 257 |
| Single-exon transcripts | 2,887 | 1,165 | 942 | 147 | 12,731 |
| coding transcripts (NM_/XM_ ) | 2,871 | 1,166 | 942 | 147 | 12,731 |
| non-coding transcripts (NR_/XR_ ) | 16 | 906 | 472 | 152 | 3,252 |
| CDSs | 26,950 | 1,783 | 1,242 | 66 | 106,596 |
| Exons | 235,837 | 295 | 138 | 1 | 19,868 |
| in coding transcripts (NM_/XM_ ) | 206,346 | 265 | 134 | 1 | 19,868 |
| in non-coding transcripts (NR_/XR_ ) | 31,131 | 496 | 178 | 1 | 16,529 |
| Introns | 205,146 | 4,849 | 1,356 | 25 | 1,010,885 |
| in coding transcripts (NM_/XM_ ) | 183,439 | 4,825 | 1,331 | 25 | 1,010,885 |
| in non-coding transcripts (NR_/XR_ ) | 23,220 | 4,968 | 1,591 | 30 | 427,076 |
Transcripts per gene, exons per transcript
| Mean | Median | Min | Max | |
|---|---|---|---|---|
| Number of transcripts per gene | 1.33 | 1 | 1 | 42 |
| Number of exons per transcript | 8.49 | 5 | 1 | 345 |
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 |
|---|---|---|---|
| Rnor_5.0 | GCF_000001895.4 | 38.05% | 29.13% |
| Rn_Celera | GCF_000002265.2 | 41.49% | 31.75% |
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
RefSeq transcript alignment quality report
The known RefSeq transcripts (NM_ and NR_ accessions) are a set of hiqh-quality transcripts maintained by the RefSeq group at NCBI. Alignment statistics for this group of transcripts, such as percent and number of sequences not aligning at all, percent best alignments split between multiple scaffolds, and percent alignments not covering the full CDS are indicative of the genome quality and are provided below.
| Rnor_5.0 Primary Assembly | Rn_Celera Primary Assembly | |
|---|---|---|
| Number of sequences retrieved from Entrez | 17,953 | 17,953 |
| Number (%) of sequences not aligning | 33 (0.18%) | 31 (0.17%) |
| Number (%) of sequences with multiple best alignments (split genes) | 255 (1.42%) | 96 (0.54%) |
| Number (%) of sequences with CDS coverage
< 95% | 961 (5.52%) | 700 (4.05%) |
Short read transcript alignments
The following short reads (RNA-Seq) from the Short Read Archive were also used for gene prediction:
Hide alignments statisticsProtein alignments
| Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by ProSplign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
|---|---|---|---|---|---|
Mus musculus known RefSeq (NP_) | 27,452 | 27,151 (98.90%) | 27,095 (98.70%) | 78.11% | 83.93% |
| Same-species GenBank | 19,698 | 18,430 (93.56%) | 18,410 (93.46%) | 81.19% | 86.58% |
Same-species known RefSeq (NP_) | 17,472 | 17,285 (98.93%) | 17,236 (98.65%) | 81.34% | 84.96% |
Homo sapiens known RefSeq (NP_) | 36,184 | 35,085 (96.96%) | 35,014 (96.77%) | 76.40% | 81.84% |
| Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by ProSplign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
|---|---|---|---|---|---|
Mus musculus known RefSeq (NP_) | 27,452 | 27,169 (98.97%) | 27,141 (98.87%) | 78.03% | 84.26% |
| Same-species GenBank | 19,698 | 18,427 (93.55%) | 18,406 (93.44%) | 81.15% | 87.02% |
Same-species known RefSeq (NP_) | 17,472 | 17,287 (98.94%) | 17,260 (98.79%) | 81.17% | 85.24% |
Homo sapiens known RefSeq (NP_) | 36,184 | 35,112 (97.04%) | 35,080 (96.95%) | 76.35% | 82.12% |
Assembly-assembly alignments of alternate to reference assembly
When multiple assemblies of good quality are available for the organism, the annotation of all is done in coordination. The alternate assemblies are aligned to the reference assembly and the best reciprocal best hits are used to identify corresponding regions, that can then be annotated together.
Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.
| First Pass | Total |
|---|---|
| Rn_Celera (Alternate) Coverage: 93.78% | Rn_Celera (Alternate) Coverage: 94.41% |
| Rnor_5.0 (Reference) Coverage: 90.84% | Rnor_5.0 (Reference) Coverage: 94.30% |
| Percent Identity: 99.93% | Percent Identity: 99.81% |
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