RetrogeneDB ID: | retro_mmul_1687 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 3:74911245..74913039(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMU.4430 | ||
| Ensembl ID: | ENSMMUG00000018037 | ||
| Aliases: | None | ||
| Description: | vacuolar protein sorting-associated protein 33A [Source:RefSeq peptide;Acc:NP_001244777] |
Retrocopy-Parental alignment summary:
>retro_mmul_1687
ATGGCGGCGCACCTGTCATACCGGCGAGTGAACCTAAACGGGCTGCGCCAGGCGGTGTATCGCGAGCTGTGCGAGTTCCT
GGACAAGTGCGCAAGAAGCAAGGGAATAGTTTGGGATGAATACCTAACTGGACTCTTTGGCCTGACTGCACAGTATTCAC
TATTGAAGGGACATGAAGTGAAAAAAAATGTTCACACTTAAAGGAAATCGTTTGCTGCAGCTGATGTCAAGAATATTATT
ATTATTATTTTTGTCAGACCCAGGCTAGAGTTGATGGATATAATTGCTGAAAACGTGCTCGGTGAAGATAGACGAGGCCC
AACGAGAGATACTCATATTCTGTTTGTGCCACAGCGTAGCCTGTTGTGTGAACAGCGGTTGAAGGATCTGGGTGTCTTGG
GATCCTTTATTCATAGGGAGGAGTACAGCTTAGATCTCATTCCATTCTATGGTAATCTCTTATCCATGGAATCAGAGGGT
GTGTTCAAAGAGTGCTACCTGGAGGGCGACCAGACGAGCCTGTACCATGCAGCCAAGGGGCTGATGACCCTGCACGCTCT
GTATGGAACGATCCCCCAGATCTTTGGGAAAGGAGAATGTGCTCAGCAAGTGGCCGATATTATGATCAGGATGAAGAGAG
AGTTTACAGGAAGCCAGAATTCAATATTACCTGTTTTTGATAGTCTCTCGTTGCTTGATCGGTGTGTGGATTTATTAACA
CCTCTTGCCACTCAGCTGACATATGAAGGACTCATTGATGAAATTTATGGCATTCAGAACAGTTATGTGAAATTATCTCC
AGAGAAATTTGCACTTAAGAAACAGGGCGATGGTGGTAAGGACCTCCTCAAGGAACAAAGAAGCTGCAGCTGAATTCTGC
AGAGGAGCTCTATGCTGAGATCCGAGACAAGAACTTCAAGGCGGTGGGCTCTGTGCTCAGCAAGAAAGCAAAGATCATCT
TGGCAGCATTCGAGGAAAGACACAATGCTAAGACCGTGGGGGAGACCAAGTAGTTTGTTTCCCAGCTGCCCCACATGCAG
GCAGCAAGGGGCTCGCTTGCAAACCATACCTCAATTGCAGAATTGATGAAAGATGTCACTACTTCTGAAGACTTTTTTGA
TAAATTAACCGTGGAACAGGAATTTATGTCTGGAATAGACACTGATAAGGTCAACAACTACACTGAGGATTGTATTGCCC
CAAAACACTCATTGATCAAGGTGTTAAGACTAGTTTGCCTCCAATCCGTGTGTAATAGTGGGGCTCAAACAAAAACTTTT
GGAATATTACAAAAGAGAGATTCTCCAGACTTACGGCTTTGAGCACATGTTGACCTTACACAACCTGGAGAAGGCCGGCC
TGCTGAAACCGCAGACGGGGGGCAGAAACAATTACCCAACTATACGGAAAACATTAGCCCTCTGGATGGATGATGTTAAG
GAGCAAAACCCCAAGGACATATCCTATATGTACAGTGGGTATGCCCTGCTCAGTGTGCGGCTGGCCCAGCTGGTTTCCCG
ACCTGGCTGGCGGAGCATCGATGAGGTCCTCTGCATCCTCCCAGGGCCCCACTTTGAGGAGCGGCAGCCACTGCCCACAG
GACTGCAGAAGAAACGTCAACCGGGAGAAAACCGAGTGACTCTGATATTTTTCCTCGGGGGCATAACCTTTGCTGAAATT
GCTGCCGTGCGATTTCTCTCCTAGTTGGAAGATGGAGGTACAGAATATGTCATTACCACCACTAAACTAATGAACGGAAC
CAGTTGGATAGAGGTTCTGATGGAAAAACCTTTC
ORF - retro_mmul_1687 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.7 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAHLSYGRVNLNVLREAVRRELREFLDKCAGSKAIVWDEYLTGPFGLIAQYSLLKEHEVEKM-FTLKGN |
| MAAHLSY.RVNLN.LR.AV.REL.EFLDKCA.SK.IVWDEYLTG.FGL.AQYSLLK.HEV....FTLKGN | |
| Retrocopy | MAAHLSYRRVNLNGLRQAVYRELCEFLDKCARSKGIVWDEYLTGLFGLTAQYSLLKGHEVXXX>FTLKGN |
| Parental | RL-PAADVKNIIFF--VRPRLELMDIIAENVLSEDRRGPTRDFHILFVPRRSLLCEQRLKDLGVLGSFIH |
| RL..AADVK.......VRPRLELMDIIAENVL.EDRRGPTRD.HILFVP.RSLLCEQRLKDLGVLGSFIH | |
| Retrocopy | RL<AAADVKXXXXXXXVRPRLELMDIIAENVLGEDRRGPTRDTHILFVPQRSLLCEQRLKDLGVLGSFIH |
| Parental | REEYSLDLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMM |
| REEYSLDLIPF.G.LLSMESEG.FKECYLEGDQTSLYHAAKGLMTL.ALYGTIPQIFGKGECA.QVA..M | |
| Retrocopy | REEYSLDLIPFYGNLLSMESEGVFKECYLEGDQTSLYHAAKGLMTLHALYGTIPQIFGKGECAQQVADIM |
| Parental | IRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQLTYEGLIDEIYGIQNSYVKLPPEKFAPKKQGDG |
| IRMKREFTGSQNSI.PVFD.L.LLDR.VDLLTPLATQLTYEGLIDEIYGIQNSYVKL.PEKFA.KKQGDG | |
| Retrocopy | IRMKREFTGSQNSILPVFDSLSLLDRCVDLLTPLATQLTYEGLIDEIYGIQNSYVKLSPEKFALKKQGDG |
| Parental | GKDL-PTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHNAKTVGEIKQFVSQLPHMQ |
| GKDL.P...KKLQLNSAEELYAEIRDKNF.AVGSVLSKKAKII.AAFEERHNAKTVGE.K.FVSQLPHMQ | |
| Retrocopy | GKDL<PQGTKKLQLNSAEELYAEIRDKNFKAVGSVLSKKAKIILAAFEERHNAKTVGETK*FVSQLPHMQ |
| Parental | AARGSLANHTSIAELIKDVTTSEDFFDKLTVEQEFMSGIDTDKVNNYIEDCIAQKHSLIKVLRLVCLQSV |
| AARGSLANHTSIAEL.KDVTTSEDFFDKLTVEQEFMSGIDTDKVNNY.EDCIA.KHSLIKVLRLVCLQSV | |
| Retrocopy | AARGSLANHTSIAELMKDVTTSEDFFDKLTVEQEFMSGIDTDKVNNYTEDCIAPKHSLIKVLRLVCLQSV |
| Parental | CNS-GLKQKVLDYYKREILQTYGYEHILTLHNLEKAGLLKPQTGGRNNYPTIRKTLRLWMDDVNEQNPTD |
| CNS.GLKQK.L.YYKREILQTYG.EH.LTLHNLEKAGLLKPQTGGRNNYPTIRKTL.LWMDDV.EQNP.D | |
| Retrocopy | CNS>GLKQKLLEYYKREILQTYGFEHMLTLHNLEKAGLLKPQTGGRNNYPTIRKTLALWMDDVKEQNPKD |
| Parental | ISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPTGLQKKRQPGENRVTLIFFLGGVT |
| ISY.YSGYA.LSVRLAQL.SRPGWRSI.EVL.ILPGPHFEERQPLPTGLQKKRQPGENRVTLIFFLGG.T | |
| Retrocopy | ISYMYSGYALLSVRLAQLVSRPGWRSIDEVLCILPGPHFEERQPLPTGLQKKRQPGENRVTLIFFLGGIT |
| Parental | FAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF |
| FAEIAA.RFLS.LEDGGTEYVI.TTKLMNGTSWIE.LMEKPF | |
| Retrocopy | FAEIAAVRFLS*LEDGGTEYVITTTKLMNGTSWIEVLMEKPF |
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 | 81 .80 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 79 .89 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 56 .63 RPM |
| SRP007412_heart | 0 .00 RPM | 40 .75 RPM |
| SRP007412_kidney | 0 .12 RPM | 56 .81 RPM |
| SRP007412_liver | 0 .00 RPM | 40 .45 RPM |
| SRP007412_testis | 0 .30 RPM | 204 .56 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1687 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1687 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_1687 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 | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000018037 | 1 retrocopy |
retro_mmul_1687 ,
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