RetrogeneDB ID: | retro_mmus_1973 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:130880865..130882130(+) | ||
| Located in intron of: | ENSMUSG00000085566 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000080989 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Psmd11 | ||
| Ensembl ID: | ENSMUSG00000017428 | ||
| Aliases: | Psmd11, 1700089D09Rik, 1810019E17Rik, 2610024G20Rik, 2810055C24Rik, C78232, P44.5, S9 | ||
| Description: | proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 [Source:MGI Symbol;Acc:MGI:1916327] |
Retrocopy-Parental alignment summary:
>retro_mmus_1973
ATGGCGGCCGCAGCGGTGGTGGAGTTCCAGAGAGTCCAGTCTCTACTTAGCACCGACCGGGAGGCCTCCATCGACATCCT
CCACTCCATCGTGAAACATGACAATCAAGAAAATGATGAGGAGGCAGTCCAGGTCAAAGAGCAGAGCATCCTTGAACTGG
GTTCTCTCCTGGCGAAGACTGGACAAGCTGATGAGCTTGGAGGACTCCTGAAGTATGTACGACCTTTCTTGAATTCCATC
AGTAAACTAAAGCAGCTCGTCTGGTCCGGTCTCTTCTTGATCTGTTTCTAGATATGGAAGCAGCTACAGGGCAGGAGGTC
GAGCTATGTTTAGAGTGCATCGAATGGGCCAAATCAGAGAAAAGAACTTTCTTACGCCAAGCATTGGAGGCAAGGCTGGT
GTCTTTGTATTTTGATACCAAGAGGTACCAGGAAGCATTGCATTTGGGTTCTCAGCTGCTTCGGGAGTTGAAAAAGATGG
ATGATAAAGCCCTTTTGGTGGAAGTACAGCTTTTAGAAAGCAAAACTTACCATGCTCTGAGTAATCTGCTGAAAGCCCGA
GCTGCCTTAACCTCTGCTCGAACCACAGCAAATGCCATCTACTGTCCCCCTAAATTGCAGGCCACCCTGGACATGCAGTC
AGGTATTATTCATGCAGCAGAGGAGAAGGACTGGAAAACTGCATACTCATACTTCTATGAGGCATTCGAAGGCTACGACT
CCATTGATAGCCCCAAGGCCATCACATCTCTGAAGTAGATGTTGCTGTGCAGAATCATGCTCAACACCCCAGAAGATGTC
CAGGCTTTGGTGAGCAGAAAGCTTGCACTTCGGTGTGCAGGGAGGCAGACAGAAGCATTGAAATGTGTGGCTCAAGCTAG
CAAGAACAGATCACTGGCAGATTTTGAAAAGGCCCTGACAGACTACAGGGCAGAGCTCCGGGACGACCCAATCATCAGCA
CACATTTGGCCAAGTTGTACAATAACTTACAGGAACAGAATCTGATCCGGGTTATTGAGTCTTTTTCCCGAGTCCAGATT
GAACACATATCTAGCCTCATCAAACTCTCCAAGGCCGACGTGGAGAGAAAATTATCACAGATGATTCTTGACAAAAAGTT
TCATGGGATTTTGGACCAGGGGGAGGGTGTCCTGATCATTTTCGATGAACCCCTAGTAGATAAAACTTATGAAGCTGCTC
TGGAAACTATTCAGAACAGGAGTAAAGTAGTGGACTCCCTCTACAGCAAAGCCAAGAAGCTGACA
ORF - retro_mmus_1973 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.22 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAAAVVEFQRAQSLLSTDREASIDILHSIVKRDIQENDEEAVQVKEQSILELGSLLAKTGQAAELGGLL |
| MAAAAVVEFQR.QSLLSTDREASIDILHSIVK.D.QENDEEAVQVKEQSILELGSLLAKTGQA.ELGGLL | |
| Retrocopy | MAAAAVVEFQRVQSLLSTDREASIDILHSIVKHDNQENDEEAVQVKEQSILELGSLLAKTGQADELGGLL |
| Parental | KYVRPFLNSISK-AKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSEKRTFLRQALEARLVSLYFD |
| KYVRPFLNSISK..KAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSEKRTFLRQALEARLVSLYFD | |
| Retrocopy | KYVRPFLNSISK<TKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSEKRTFLRQALEARLVSLYFD |
| Parental | TKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKLQAT |
| TKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHALSNL.KARAALTSARTTANAIYCPPKLQAT | |
| Retrocopy | TKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHALSNLLKARAALTSARTTANAIYCPPKLQAT |
| Parental | LDMQSGIIHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRY |
| LDMQSGIIHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLK.MLLC.IMLNTPEDVQALVS.KLALR. | |
| Retrocopy | LDMQSGIIHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLK*MLLCRIMLNTPEDVQALVSRKLALRC |
| Parental | AGRQTEALKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEH |
| AGRQTEALKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLY.NL.EQNLIRVIE.FSRVQIEH | |
| Retrocopy | AGRQTEALKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLYNNLQEQNLIRVIESFSRVQIEH |
| Parental | ISSLIKLSKADVERKLSQMILDKKFHGILDQGEGVLIIFDEPPVDKTYEAALETIQNMSKVVDSLYSKAK |
| ISSLIKLSKADVERKLSQMILDKKFHGILDQGEGVLIIFDEP.VDKTYEAALETIQN.SKVVDSLYSKAK | |
| Retrocopy | ISSLIKLSKADVERKLSQMILDKKFHGILDQGEGVLIIFDEPLVDKTYEAALETIQNRSKVVDSLYSKAK |
| Parental | KLT |
| KLT | |
| Retrocopy | KLT |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 1 .57 RPM | 56 .63 RPM |
| SRP007412_cerebellum | 0 .96 RPM | 56 .19 RPM |
| SRP007412_heart | 0 .97 RPM | 53 .82 RPM |
| SRP007412_kidney | 1 .66 RPM | 58 .85 RPM |
| SRP007412_liver | 1 .67 RPM | 61 .72 RPM |
| SRP007412_testis | 1 .14 RPM | 50 .04 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1973 was not detected
1 EST(s) were mapped to retro_mmus_1973 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| BE457074 | 130880868 | 130881429 | 99.9 | 560 | 1 | 559 |
No TSS is located nearby retro_mmus_1973 retrocopy 5' end.
retro_mmus_1973 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1973 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014450 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000017428 | 1 retrocopy |
retro_mmus_1973 ,
|
| Tupaia belangeri | ENSTBEG00000001962 | 1 retrocopy |