RetrogeneDB ID: | retro_mmus_2564 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:43916752..43918228(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000093859 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Apex2 | ||
| Ensembl ID: | ENSMUSG00000025269 | ||
| Aliases: | Apex2, C430040P13Rik, ape2 | ||
| Description: | apurinic/apyrimidinic endonuclease 2 [Source:MGI Symbol;Acc:MGI:1924872] |
Retrocopy-Parental alignment summary:
>retro_mmus_2564
ATGTTATGCATGGTAAACTGGGACATCAATGGGATTCGGAGACCCCTGCAAGGTCTGGGATGCAAGGTGCCCAGCAACTG
TCCCACGGCCTTGAGATACATTTTAGAGGAGCTGGATGGCGATATTTTCTGTCTCCAGGAGACCAAAGTGAGCAGAGATG
CGCTGACGGAGCCCTTGGCTTTTGTTGAGGGCTATAACTCCTATTTCAGCTTCAGTCACAGCCGGAGTGGCTATCCTGGT
GTAGCTACTTTCTGTAAGGACAGTGTTACATCCGTGGCTGCTGAAGAAAGCCTGAGTGGTCAGTTTGCCACCCTGAACCG
GCATGTCGGTTGCTATGGAAACATGACCGCGTTCACCCAAGAGCAGCTACAGGCTCTGGATATCGAGGGCTGAGCTGTCC
TTACACCACAGCAAAAGGTCTTCACACAGGAAGAGAAGGGGAAGCCTTTGACCCTGATCAATGTGTACTGCCTGTGTACC
GATCCTAGGAACCCGGAGTGGCTGATCTTTAAGATGCATTTCTATCGCTTGCTGCAAATCCGAGCAGAAGCACTCCTGGC
AGCCGGCAGTCATGTGATAATCCTGGGGGGCATGAATATAGCGTACTGTCCCATTGACCACTGTGATGCTGGCGGTCTGG
GGTGCTTTGAAGAAGTCCTGGGTCGTAAGAGGATGGATGGCTTGCTTAGTAACCCGGAATACCAGGCTGGGTCCCATATA
GGACCTTTCATGGATAGCTATCTCTATTTCTATCCAAAACAGGAGAGGGCCTTTACCTGCTGGTCAGTGATCAGTAGTGT
CCGCAATCTCAACTATGGCACCCGACTTGACTACATACTGGGATACAGGACTCTAACTATAGACACTTTCCAAGATGCCT
TCCTGCTCCCTGAGATGATGGGCTCTGACCACTGCCCTGTGGAAGCTGTCTTGCATGTGTCCTGTATGCCAGCAAAGCAG
TGCCCAGCTCTGTGCACCCATTTTCTCCCCGAGTTTGCAGGTACCCAGCTCAAGATTCTTGGCTTCCTAGTCCCTTGTGA
ACAAGAACCTATGTGGTGGCAGCCAGTCCTGCAGCCCAGCAAACAAGTCCAGCTACAGAAAAAGAGAAAAGCCCACAGGC
ACTCATCCAGGCCTCGAAAGCATCAAGGTGGTCCCAGAAAACACCAGAAAAACCTGATGAGTTATTTTCAGCCTTCTGTT
AGCTTTTCCCAGACTTTTGGTGTGGAACTACCTAAGCTGCCTCTGGTGGGCACTCTTGTAACTCCAACAACTCTGGAAGG
GGATGTGATAGCCACAAAGAAGGATAAGCAGGCCAAGGTTTCTGAGGTCAGAAATGAGGAGGAGGCACAGACCTCATTCT
GGAAATCTGTGCTGAGTGGGCCCTCAGCCACGCCCCTCTGCAGAGGCCACAGGGAGCCATGTGTGATGTGGATTGTGAAA
AAAACAGGATCCAACCTGGGCCGCCATTTCTTTCTT
ORF - retro_mmus_2564 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.59 % |
| Parental protein coverage: | 95.35 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MLRVVSWNINGIRSPLQGLACQEPSSCPTALRRVLDELDADIVCLQETKVTRDVLTEPLAIVEGYNSYFS |
| ML..V.W.INGIR.PLQGL.C..PS.CPTALR..L.ELD.DI.CLQETKV.RD.LTEPLA.VEGYNSYFS | |
| Retrocopy | MLCMVNWDINGIRRPLQGLGCKVPSNCPTALRYILEELDGDIFCLQETKVSRDALTEPLAFVEGYNSYFS |
| Parental | FSRSRSGYSGVATFCKDSATPVAAEEGLSGVFATLNGDIGCYGNMDEFTQEELRVLDSEGRALLT-QHKI |
| FS.SRSGY.GVATFCKDS.T.VAAEE.LSG.FATLN...GCYGNM..FTQE.L..LD.EG.A.LT.Q.K. | |
| Retrocopy | FSHSRSGYPGVATFCKDSVTSVAAEESLSGQFATLNRHVGCYGNMTAFTQEQLQALDIEG*AVLTPQQKV |
| Parental | RTLEGKEKTLTLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPIDHCDA |
| .T.E.K.K.LTLINVYC...DP..PE.L.FKM.FYRLLQ.RAEALLAAGSHVIILG..N.A..PIDHCDA | |
| Retrocopy | FTQEEKGKPLTLINVYCLCTDPRNPEWLIFKMHFYRLLQIRAEALLAAGSHVIILGGMNIAYCPIDHCDA |
| Parental | SSLECFEEDPGRKWMDGLLSNPGDEAGPHIGLFMDSYRYLHPKQQRAFTCWSVVSGARHLNYGSRLDYVL |
| ..L.CFEE..GRK.MDGLLSNP...AG.HIG.FMDSY.Y..PKQ.RAFTCWSV.S..R.LNYG.RLDY.L | |
| Retrocopy | GGLGCFEEVLGRKRMDGLLSNPEYQAGSHIGPFMDSYLYFYPKQERAFTCWSVISSVRNLNYGTRLDYIL |
| Parental | GDRALVIDTFQASFLLPEVMGSDHCPVGAVLNVSCVPAKQCPALCTRFLPEFAGTQLKILRFLVPLEQEP |
| G.R.L.IDTFQ..FLLPE.MGSDHCPV.AVL.VSC.PAKQCPALCT.FLPEFAGTQLKIL.FLVP.EQEP | |
| Retrocopy | GYRTLTIDTFQDAFLLPEMMGSDHCPVEAVLHVSCMPAKQCPALCTHFLPEFAGTQLKILGFLVPCEQEP |
| Parental | VREQQVLQPSHQIQAQRQPRKAFMHSTRLRKSQGGPKRKQKNLMSYFQPSSSLSQTSGVELPTLPLVGPL |
| ...Q.VLQPS.Q.Q.Q...RKA..HS.R.RK.QGGP...QKNLMSYFQPS.S.SQT.GVELP.LPLVG.L | |
| Retrocopy | MWWQPVLQPSKQVQLQKK-RKAHRHSSRPRKHQGGPRKHQKNLMSYFQPSVSFSQTFGVELPKLPLVGTL |
| Parental | TTPKTAEEVATATMLEEKNKVPESKDEKGERTAFWKSMLSGPSPMPLCGGHREPCVMRTVKKTGPNFGRQ |
| .TP.T.E....AT......KV.E...E....T.FWKS.LSGPS..PLC.GHREPCVM..VKKTG.N.GR. | |
| Retrocopy | VTPTTLEGDVIATKKDKQAKVSEVRNEEEAQTSFWKSVLSGPSATPLCRGHREPCVMWIVKKTGSNLGRH |
| Parental | FYM |
| F.. | |
| Retrocopy | FFL |
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 | 0 .00 RPM | 5 .28 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .17 RPM |
| SRP007412_heart | 0 .03 RPM | 5 .82 RPM |
| SRP007412_kidney | 0 .00 RPM | 9 .51 RPM |
| SRP007412_liver | 0 .00 RPM | 6 .80 RPM |
| SRP007412_testis | 0 .09 RPM | 1 .42 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2564 was not detected
No EST(s) were mapped for retro_mmus_2564 retrocopy.
No TSS is located nearby retro_mmus_2564 retrocopy 5' end.
retro_mmus_2564 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2564 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016584 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000016298 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000025269 | 1 retrocopy |
retro_mmus_2564 ,
|
| Mus musculus | ENSMUSG00000035960 | 2 retrocopies | |
| Rattus norvegicus | ENSRNOG00000000166 | 1 retrocopy |