RetrogeneDB ID: | retro_mmus_3491 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:100329691..100330276(+) | ||
| Located in intron of: | ENSMUSG00000059327 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083936 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Zfyve19 | ||
| Ensembl ID: | ENSMUSG00000068580 | ||
| Aliases: | Zfyve19, 1500041L05Rik | ||
| Description: | zinc finger, FYVE domain containing 19 [Source:MGI Symbol;Acc:MGI:1919258] |
Retrocopy-Parental alignment summary:
>retro_mmus_3491
ATGGAGAGCAGGTGCTACGGCTGTGCTGTCCAGTTTACCCTCTTCAAGGAGTATGGCTGTAAGAATTGTGGCCAAGCCTT
CTGTAAGGACTCTCTTAGCTTCAGTGTTCTGCTACCCCAGACTGGCAACACATAACAGAAAGTCTGCAAGCAGTGCCACA
CAGTCCTGACCAGAGGATCCTCCAAGTGATCGCCACCTCAGTATAAGAAGTGTGTGGCAGCCTTGGAAGACAAGAAGAAG
CCCAGCACTTCCTAGAGCCAAGGCCTGACCCACAAAGACAAAGACATTGCTGAGTGCCTAGCAGGAATTTGGCCGGAAAA
CAAGCCCAAGTCAGTACCCTCACAAGCAGAGATAGAGGCACAGCTAGCCACGCTGAAGGATGAAGTCCAGGGCCCCATTC
CTACCACACAGGAGATGGAGGATCAGCTTGCAGCATTGCAGGGCACAGTCCTGCTTCTTCACACTTTGAGGCTGGCACAC
CAGGCACCAGATATCAGGACCCAAGGCCAGCAGATGCAGAATCTGCTAACACAGTTGACAGCTGAGGTGGATATTGATGA
AAGCTGGCAACCAAGAGCCTCAGCC
ORF - retro_mmus_3491 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.62 % |
| Parental protein coverage: | 51.67 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILTRGSSDNASKWSP |
| MESRCYGCAV.FTLFK.EYGCKNCG.AFC...LSFS.L.P..GNT.QKVCKQCHT.LTRGS....SK.SP | |
| Retrocopy | MESRCYGCAVQFTLFK-EYGCKNCGQAFCKDSLSFSVLLPQTGNT*QKVCKQCHTVLTRGS----SK*SP |
| Parental | PQNYKKRVAALEAKKKSSTSHSQSLTHKDQAIAERLARLRQENKPKSVPSQAEIEARLAALKDEVQGPIP |
| PQ.YKK.VAALE.KKK.STS.SQ.LTHKD..IAE.LA....ENKPKSVPSQAEIEA.LA.LKDEVQGPIP | |
| Retrocopy | PQ-YKKCVAALEDKKKPSTS*SQGLTHKDKDIAECLAGIWPENKPKSVPSQAEIEAQLATLKDEVQGPIP |
| Parental | STQEMEDRLAALQGRVPPSHTVRPAHQAPDTRTQAQQTQDLLTQLTAEVAIDENCQPRASA |
| .TQEMED.LAALQG.V...HT.R.AHQAPD.RTQ.QQ.Q.LLTQLTAEV.IDE..QPRASA | |
| Retrocopy | TTQEMEDQLAALQGTVLLLHTLRLAHQAPDIRTQGQQMQNLLTQLTAEVDIDESWQPRASA |
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 .02 RPM | 12 .29 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 13 .94 RPM |
| SRP007412_heart | 0 .00 RPM | 6 .82 RPM |
| SRP007412_kidney | 0 .00 RPM | 11 .84 RPM |
| SRP007412_liver | 0 .00 RPM | 9 .26 RPM |
| SRP007412_testis | 0 .00 RPM | 20 .35 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3491 was not detected
No EST(s) were mapped for retro_mmus_3491 retrocopy.
No TSS is located nearby retro_mmus_3491 retrocopy 5' end.
retro_mmus_3491 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3491 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000068580 | 1 retrocopy |
retro_mmus_3491 ,
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