RetrogeneDB ID: | retro_mmus_2401 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:144296900..144298034(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000095960 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Zmynd11 | ||
| Ensembl ID: | ENSMUSG00000021156 | ||
| Aliases: | Zmynd11, 2210402G22Rik, BS69 | ||
| Description: | zinc finger, MYND domain containing 11 [Source:MGI Symbol;Acc:MGI:1913755] |
Retrocopy-Parental alignment summary:
>retro_mmus_2401
CTGGTCCATTCAGCTGTTGATGTCCCTCCCATACAAGGAAGGTGAATGAGGGGAAGTACTGGAGTTAAGTGGAGTTCAAG
GCTGACACACAGCTGCTTCTGCACAACAGTGATCTGCTATGGAGCAGGGAGCCAGGGGACATTGCAAGTATGTGATATAA
AGACACGTACCATGAGCTGGACAAGCTGCAGCTTTGCAAGAACTGCTTCTACCTGTCAAACCCACGGCCCGACAACTGGT
TCTGCTACCCTTGCATATCTAATCATGAGCTGCTTTGGGCTAAAATAAAAGGTTTTGGGGTTTGGCCAGCCAAAGTCATG
CAGAAAGAAGACAGTCAAGTTTGTGTTCGCTTCTTTGGCCATACCACCAGAGAGCCTGGATTCCTTTTGAAAATATTCAG
GATATTACAGTCAATGTTCACAGATTACATGTGAAGCACAGCATGGGCTTGAAAAAGGCCAGTGATGAGCTGGAACTGCA
TCAGGGCTTCGTCCATGAAGGAAGGTTCTGGAAGTCTAAGAATGATGACTGAGGTGAGAAAGAGACAGAATCCAGTATCT
CCTTGACCAGTTATGAACCGCTGAAGGTCACTCAAGAGCCAAGAGCAAAGAAAGGACGATGTAATCAGAGTGTGGAGCCC
AGAAAGGAAGAACCCGAGCCAGAAATGGAAGCAGTAAGTTTCAGACAGGAAATCCCCACAATGCCTCAGCCAGTTGACAG
GGTGTCAGTATCAACCCAGACCAGGAAGTTAAGTGCCTCTTCCCCAGGAATGCTGCATCTGCATCGAAGTACTAGGATGA
CGAGAGACGGTGTCTTTCAGAGCATGTGCCACGACAAGTATACCAAAAATTTTAATGACTTTAAAGACAGGATGAAGTCG
GAACACAAGCGGGAAACAGAGAGAGTGGTCTGTACAGTGCTGGAAAAGTTGCGTTCTGAAATGGAAGAAGAAAAAGACAA
GCCGTGAACAAAGCTGTAGCCAACCTGCAGGCTGAGATGCACAGAAAGTGTAAGCAGGTGAAGGAAAAGTGTAAGGAAGC
ATTTGTAGAGGAGATCAAGGAACTAGCGGCGCAGCACAAGCAGCTCATTTCTCAGATCAAGAAACAGTGGTGTTACAACT
GTGAGGAGGCAGCA
CTGGTCCATTCAGCTGTTGATGTCCCTCCCATACAAGGAAGGTGAATGAGGGGAAGTACTGGAGTTAAGTGGAGTTCAAG
GCTGACACACAGCTGCTTCTGCACAACAGTGATCTGCTATGGAGCAGGGAGCCAGGGGACATTGCAAGTATGTGATATAA
AGACACGTACCATGAGCTGGACAAGCTGCAGCTTTGCAAGAACTGCTTCTACCTGTCAAACCCACGGCCCGACAACTGGT
TCTGCTACCCTTGCATATCTAATCATGAGCTGCTTTGGGCTAAAATAAAAGGTTTTGGGGTTTGGCCAGCCAAAGTCATG
CAGAAAGAAGACAGTCAAGTTTGTGTTCGCTTCTTTGGCCATACCACCAGAGAGCCTGGATTCCTTTTGAAAATATTCAG
GATATTACAGTCAATGTTCACAGATTACATGTGAAGCACAGCATGGGCTTGAAAAAGGCCAGTGATGAGCTGGAACTGCA
TCAGGGCTTCGTCCATGAAGGAAGGTTCTGGAAGTCTAAGAATGATGACTGAGGTGAGAAAGAGACAGAATCCAGTATCT
CCTTGACCAGTTATGAACCGCTGAAGGTCACTCAAGAGCCAAGAGCAAAGAAAGGACGATGTAATCAGAGTGTGGAGCCC
AGAAAGGAAGAACCCGAGCCAGAAATGGAAGCAGTAAGTTTCAGACAGGAAATCCCCACAATGCCTCAGCCAGTTGACAG
GGTGTCAGTATCAACCCAGACCAGGAAGTTAAGTGCCTCTTCCCCAGGAATGCTGCATCTGCATCGAAGTACTAGGATGA
CGAGAGACGGTGTCTTTCAGAGCATGTGCCACGACAAGTATACCAAAAATTTTAATGACTTTAAAGACAGGATGAAGTCG
GAACACAAGCGGGAAACAGAGAGAGTGGTCTGTACAGTGCTGGAAAAGTTGCGTTCTGAAATGGAAGAAGAAAAAGACAA
GCCGTGAACAAAGCTGTAGCCAACCTGCAGGCTGAGATGCACAGAAAGTGTAAGCAGGTGAAGGAAAAGTGTAAGGAAGC
ATTTGTAGAGGAGATCAAGGAACTAGCGGCGCAGCACAAGCAGCTCATTTCTCAGATCAAGAAACAGTGGTGTTACAACT
GTGAGGAGGCAGCA
ORF - retro_mmus_2401 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80. % |
| Parental protein coverage: | 69.34 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LVHSAVDVPTIQ-EKVNEGKYRSYEEFKADAQLLLHNTVIFYGADSEQADIARMLYKDTCHELDELQLCK |
| LVHSAVDVP.IQ..KVNEGKY.S..EFKAD.QLLLHN.........E..DIA.M.YKDT.HELD.LQLCK | |
| Retrocopy | LVHSAVDVPPIQ<RKVNEGKYWS*VEFKADTQLLLHNSDLLWSR--EPGDIASM*YKDTYHELDKLQLCK |
| Parental | NCFYLSNARPDNWFCYPCIPNHELVWAKMKGFGFWPAKVMQKEDNQVDVRFFGH-HHQRAWIPSENIQDI |
| NCFYLSN.RPDNWFCYPCI.NHEL.WAK.KGFG.WPAKVMQKED.QV.VRFFGH..HQRAWIP.ENIQDI | |
| Retrocopy | NCFYLSNPRPDNWFCYPCISNHELLWAKIKGFGVWPAKVMQKEDSQVCVRFFGH<YHQRAWIPFENIQDI |
| Parental | TVNVHRLHVKRSMGWKKACDELELHQRFLREGRFWKSKNEDRGEEEAESSISSTSNEQLKVTQEPRAKKG |
| TVNVHRLHVK.SMG.KKA.DELELHQ.F..EGRFWKSKN.D.GE.E.ESSIS.TS.E.LKVTQEPRAKKG | |
| Retrocopy | TVNVHRLHVKHSMGLKKASDELELHQGFVHEGRFWKSKNDD*GEKETESSISLTSYEPLKVTQEPRAKKG |
| Parental | RRNQSVEPKKEEPEPETEAVSSSQEIPTMPQPIERVSVSTQTKKLSASSPRM--LHRSTQTTSDGVCQSM |
| R.NQSVEP.KEEPEPE.EAVS..QEIPTMPQP..RVSVSTQT.KLSASSP.M..LHRST..T.DGV.QSM | |
| Retrocopy | RCNQSVEPRKEEPEPEMEAVSFRQEIPTMPQPVDRVSVSTQTRKLSASSPGMLHLHRSTRMTRDGVFQSM |
| Parental | CHDKYTKIFNDFKDRMKSDHKRETERVVREALEKLRSEMEEE-KRQAVNKAVASLQGDMDRKGKQLKEKC |
| CHDKYTK.FNDFKDRMKS.HKRETERVV...LEKLRSEMEEE.KRQAVNKAVA.LQ..M.RK.KQ.KEKC | |
| Retrocopy | CHDKYTKNFNDFKDRMKSEHKRETERVVCTVLEKLRSEMEEE<KRQAVNKAVANLQAEMHRKCKQVKEKC |
| Parental | KEEFVEEIKKLAAQHKQLISQTKKKQWCYNCEEEA |
| KE.FVEEIK.LAAQHKQLISQ..KKQWCYNCEE.A | |
| Retrocopy | KEAFVEEIKELAAQHKQLISQI-KKQWCYNCEEAA |
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 | 207 .07 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 216 .67 RPM |
| SRP007412_heart | 0 .00 RPM | 138 .47 RPM |
| SRP007412_kidney | 0 .00 RPM | 141 .33 RPM |
| SRP007412_liver | 0 .00 RPM | 63 .19 RPM |
| SRP007412_testis | 0 .00 RPM | 73 .37 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_2401 was not detected
No EST(s) were mapped for retro_mmus_2401 retrocopy.
No TSS is located nearby retro_mmus_2401 retrocopy 5' end.
retro_mmus_2401 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2401 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000021156 | 2 retrocopies |
retro_mmus_2401 , retro_mmus_2523,
|