Table 6.
Comparison of NCBI annotation reports for mRatBN7.2, GRCr8, and GRCm39
| Feature | mRatBN7.2 | GRCr8 | GRCm39 |
|---|---|---|---|
| A. Genes, pseudogenes, mRNA's pseudo transcripts and CDS's annotated in the assemblies | |||
| Genes and pseudogenes | 42,054 | 47,357 | 50,561 |
| Protein-coding | 21,990 | 23,154 | 22,186 |
| Noncoding | 11,558 | 14,864 | 17,518 |
| Transcribed pseudogenes | 157 | 117 | 474 |
| Nontranscribed pseudogenes | 8005 | 8687 | 9869 |
| Genes with variants | 16,116 | 17,767 | 18,531 |
| Immunoglobulin/T cell receptor gene segments | 300 | 501 | 490 |
| Other | 44 | 34 | 24 |
| mRNAs | 73,402 | 85,576 | 92,486 |
| Fully supported | 72,688 | 84,885 | 92,206 |
| With >5% ab initio | 369 | 371 | 113 |
| Partial | 83 | 79 | 54 |
| With filled gap(s) | 0 | 0 | 0 |
| Known RefSeq (NM_) | 20,574 | 21,191 | 37,907 |
| Model RefSeq (XM_) | 52,828 | 64,385 | 54,579 |
| Noncoding RNAs | 24,927 | 30,129 | 38,629 |
| Fully supported | 21,377 | 26,261 | 35,041 |
| With >5% ab initio | 0 | 0 | 0 |
| Partial | 1 | 0 | 5 |
| With filled gap(s) | 0 | 0 | 0 |
| Known RefSeq (NR_) | 817 | 821 | 7443 |
| Model RefSeq (XR_) | 23,041 | 28,207 | 29,867 |
| Pseudotranscripts | 159 | 121 | 533 |
| Fully supported | 141 | 108 | 524 |
| With >5% ab initio | 0 | 0 | 0 |
| Partial | 0 | 0 | 0 |
| With filled gap(s) | 0 | 0 | 0 |
| Known RefSeq (NR_) | 43 | 43 | 461 |
| Model RefSeq (XR_) | 116 | 78 | 72 |
| CDSs | 73,715 | 86,077 | 92,989 |
| Fully supported | 72,688 | 84,885 | 92,206 |
| With >5% ab initio | 432 | 441 | 155 |
| Partial | 83 | 75 | 53 |
| With major correction(s) | 413 | 208 | 30 |
| Known RefSeq (NP_) | 20,574 | 21,191 | 37,920 |
| Model RefSeq (XP_) | 52,841 | 64,385 | 54,579 |
| B. featureCounts in the assemblies | |||
| Genes | 33,592 | 38,052 | 39,728 |
| All transcripts | 98,329 | 115,705 | 131,115 |
| mRNA | 73,402 | 85,576 | 92,486 |
| misc_RNA | 4637 | 4764 | 10,029 |
| miRNA | 796 | 796 | 2112 |
| tRNA | 737 | 771 | 422 |
| lncRNA | 16,266 | 21,024 | 23,611 |
| snoRNA | 1288 | 1564 | 1331 |
| snRNA | 1026 | 1013 | 999 |
| antisense_RNA | 1 | 1 | 9 |
| rRNA | 139 | 159 | 41 |
| telomerase_RNA | 1 | 1 | 64 |
| RNase_MRP_RNA | 1 | 1 | 1 |
| SRP_RNA | 1 | 1 | |
| Single-exon transcripts | 3200 | 3392 | 2941 |
| Coding transcripts (NM_/XM_) | 3179 | 3371 | 2710 |
| Noncoding transcripts (NR_/XR_) | 21 | 21 | 231 |
| Exons | 316,617 | 337,524 | 352,138 |
| In coding transcripts (NM_/XM_) | 272,844 | 284,365 | 285,412 |
| In noncoding transcripts (NR_/XR_) | 72,831 | 78,922 | 120,842 |
| Introns | 264,390 | 276,634 | 291,708 |
| In coding transcripts (NM_/XM_) | 233,700 | 240,878 | 243,819 |
| In noncoding transcripts (NR_/XR_) | 59,216 | 61,168 | 100,211 |
