RetrogeneDB ID: | retro_mmus_2523 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:144041135..144042269(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000095987 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | 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_2523
CTGGCCCATTCAGCTGTTGATGTCCCTACCATACAAGGAAGGTGAATGAGGGGAAGTACTGGAGTTAAGTGGAGTTCAAG
GCTGACACACAGCTGCTTCTGCACAACAGTGATCTGCTATGGAGCAGGGAGCCAGGGGACATTGCAAGGATGTGATATAA
AGACGCGTACCATGAGCTGGACGAGCTGCAGCTTTGCAAGAACTGCTTCTACCTGTCAAACCCACGGCCCGACAACTGGT
TCTGCTACCCTTGCATATCTAATCATGAGCTGCTTTGGGCTAAAATGAAAGATTTTGGGGTTTGGCCAGCCAAAGTCATG
CAGAAAGAATACAGTCAAGTTTGTGTTTGCTTCTTTGGCCATACCACCAGAGAGCCTGGATTCCTTTTGAAAATATTCAG
GATATTACAGTCAATGTTCACAGATTACATGTGAAGCACAGCATGGGCTTGAAAAAGGCCAGTGATGAGCTGGAACTGCA
TCAGGGCTTCCTCCATGAAGGAAGGTTCTGGAAGTCTAAGAATGATGACTGAGGTAAGAAAGAGGCAGAATCCAGTATCT
CCTTGACCAGTAATGAACCGCTGAAGGTCACTCAAGAGCCAAGAGCAAAGAAAGGACGATGTAATCAGAGTGTGGAGCCC
AGAAAGGAAGAACCCGAGCCAGAAATGGAAGCAGTAAGTTTCAGACAGGAAATCCCCACAATGCCTCAGCCAGTTGACAG
GGTGTCAGTGTCAACCCAGACCAGGAAGTTAAATGCCTCTTCCCCAGGAATGCTGCATCTGCATCAAAGCACTCAGATGA
TGAGCAATGGTGTTTGTCAGAGCATGTGCCACGACAAGTATACCAAAAATTTTAATGACTTTAAAGACAGGATGAAGTCG
GAACACAAGCGGGAAACAGAGAGAGTGGTCTGTCAAGAGCTGGAAAAGTTGCGTTCTGAAATGGAAGAAGAAAAAGACAA
GCCGTGAACAAAGCTGTAGCCAACCTGCAGGCTGAGATGCACAGAAAGTGTAAGCAGGTGAAGGAAAAGTGTAAGGAAGC
ATTTGTAGAGGAGATCAAGGAACTAGCGGCGCAGCACAAGCAGCTCATTTCTCAGATCAAGAAGCAGTGGTGTTACAACT
GTGAGGAGGCGGCA
ORF - retro_mmus_2523 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.0 % |
| Parental protein coverage: | 69.34 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LVHSAVDVPTIQ-EKVNEGKYRSYEEFKADAQLLLHNTVIFYGADSEQADIARMLYKDTCHELDELQLCK |
| L.HSAVDVPTIQ..KVNEGKY.S..EFKAD.QLLLHN.........E..DIARM.YKD..HELDELQLCK | |
| Retrocopy | LAHSAVDVPTIQ<RKVNEGKYWS*VEFKADTQLLLHNSDLLWSR--EPGDIARM*YKDAYHELDELQLCK |
| Parental | NCFYLSNARPDNWFCYPCIPNHELVWAKMKGFGFWPAKVMQKEDNQVDVRFFGH-HHQRAWIPSENIQDI |
| NCFYLSN.RPDNWFCYPCI.NHEL.WAKMK.FG.WPAKVMQKE..QV.V.FFGH..HQRAWIP.ENIQDI | |
| Retrocopy | NCFYLSNPRPDNWFCYPCISNHELLWAKMKDFGVWPAKVMQKEYSQVCVCFFGH<YHQRAWIPFENIQDI |
| Parental | TVNVHRLHVKRSMGWKKACDELELHQRFLREGRFWKSKNEDRGEEEAESSISSTSNEQLKVTQEPRAKKG |
| TVNVHRLHVK.SMG.KKA.DELELHQ.FL.EGRFWKSKN.D.G..EAESSIS.TSNE.LKVTQEPRAKKG | |
| Retrocopy | TVNVHRLHVKHSMGLKKASDELELHQGFLHEGRFWKSKNDD*GKKEAESSISLTSNEPLKVTQEPRAKKG |
| Parental | RRNQSVEPKKEEPEPETEAVSSSQEIPTMPQPIERVSVSTQTKKLSASSPRM--LHRSTQTTSDGVCQSM |
| R.NQSVEP.KEEPEPE.EAVS..QEIPTMPQP..RVSVSTQT.KL.ASSP.M..LH.STQ..S.GVCQSM | |
| Retrocopy | RCNQSVEPRKEEPEPEMEAVSFRQEIPTMPQPVDRVSVSTQTRKLNASSPGMLHLHQSTQMMSNGVCQSM |
| Parental | CHDKYTKIFNDFKDRMKSDHKRETERVVREALEKLRSEMEEE-KRQAVNKAVASLQGDMDRKGKQLKEKC |
| CHDKYTK.FNDFKDRMKS.HKRETERVV...LEKLRSEMEEE.KRQAVNKAVA.LQ..M.RK.KQ.KEKC | |
| Retrocopy | CHDKYTKNFNDFKDRMKSEHKRETERVVCQELEKLRSEMEEE<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 .04 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 .05 RPM | 73 .37 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2523 was not detected
No EST(s) were mapped for retro_mmus_2523 retrocopy.
No TSS is located nearby retro_mmus_2523 retrocopy 5' end.
retro_mmus_2523 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2523 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 ,
|