RetrogeneDB ID: | retro_mdom_1621 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 6:204355365..204356835(+) | ||
| Located in intron of: | ENSMODG00000012069 | ||
Retrocopy information | Ensembl ID: | ENSMODG00000022971 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ATXN10 | ||
| Ensembl ID: | ENSMODG00000007304 | ||
| Aliases: | None | ||
| Description: | ataxin 10 [Source:HGNC Symbol;Acc:10549] |
Retrocopy-Parental alignment summary:
>retro_mdom_1621
ATGGCGGCGCCCAGCAAGGAATCGGACCGTGCCGGACCCAGCTCCGAGCGGCTGGAGATGGCGCTGGTGGCTCTGGAAGC
CGACCATGAGCCGGGCGATCGCCTGGAGCGACTACAGGAGCTTACGGGGCTGCTCCGTGAGCAGCGGCACCGAGAAACAG
CGTCCAAGCGGGTCTTTCAGGACGTTCAACAAATCCTGACAAAATCCTCCCATGAGGTAGAGCTGGCGTGCGGGGAGGCT
GGTCGCCCATTGTACCTGGACCCCCAACTGCAGCTCACTGCAGAGTGTTTCCGCTGCCTGCGGAATGCTTGTGTGCGGTG
CGCTGGGAACCAGGACATGATCAGGGACTTGGATTTGATCGGCACCTCCGTGAAGCTGGTGGATTTATTTCAGAAACTGA
ATGTCATTAATCAGGAATCCCGGCTGACAGCCTTTCGATGTGGCCTGCAGTTCTTGGGCAATGCTGTGGCAGGAAATGAG
GCTTCTCAGAGGATGCTGTGGAAAGATGCCTTCCCAGATCTCTTCTTGGGCTGCCTCAGCTATTCAGATGAGAAGATTGT
CACCTACTCTTGCATGATCCTGTTCACGTGTCTGAACTCGGAGAGGCTGAAGGACCTTCAGAGCAGAAATCTGACCGTAG
CTTTGAGAGTTGTCCAGGCCTACCAGAAGCTGGCAGATGCTGATTGGGCCTTCTTGATCATTTCAGAGTATTTGCTGAGA
AGCCCAGAGCTGGTGAACTCCCTCTATGCTAAGCTGAGCCATCAGGAAAGGGTGGCCTTGCTCGATCTCATGATAGCCAA
ACTTGTAGGGGATGAGCCACTGACCAGTGAGTTCACAGCTGCATTTCTAAGTCACACTGGATTTGTGGCAAGCAGATTCC
AGGAGAAATGCAAGTCTGTGCTGAAGCTTGCCTCCTCCGACCACAGTGGTGATGAGGAAGCCCTGACCACCATTAGGCTT
CTCCATGTCCTTTGTGAAATGAGTGCCAACTGTGACCTGCTCCCCTCCTTACAAGCTTTCCCTGGGCTCCTCCAGACAGC
AGTTGAGACCTTGCAGATGACTCATTTGGCAGGGAAGCAGACCCCAAATGTCTTCACCACTTCTCCCTGTGTGCGTGGGG
AAGGGGACATCTCCAGCCCTGTGGCAGGGTTCAAGTCCCACCTCATTCGTCTGATTGGCAACTTGTGCTATAAAGATAAG
AATAACCAAGACAAAGTGTATCAATTAGATGGTATCCCCCTGATTCTGGACAGCTGCAGCATGGATGACAACAATCCCTT
TCTGAAAGAGTGGGCAGTGTATGCCATTCGAAATCTGACTGAGCAGAATAAGAGAAACCAAGAACTAATTGCAAAGATGG
AAAATCACGGCCTGGCAGATACAGCCATGTTGAAGAAAATGGGTCTAGAAGTTGAACAAAGAGATGGGAAGCTTACTGTG
AGATCCACAAGAAAAGCTTCTGGTGGTAAA
ORF - retro_mdom_1621 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.94 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAPSEELDRVGTSSGLVESALMTLEADNEPDKQLERLQELMGLLREQRHRETASKQVFQDIKQILTKSS |
| MAAPS.E.DR.G.SS...E.AL..LEAD.EP...LERLQEL.GLLREQRHRETASK.VFQD..QILTKSS | |
| Retrocopy | MAAPSKESDRAGPSSERLEMALVALEADHEPGDRLERLQELTGLLREQRHRETASKRVFQDVQQILTKSS |
| Parental | HEVELACRETGHLVYLDPHLQLIAECFRCLRNACVQCPGNQDMIRDLDLIGTSMKLMYLFQKLNVIKQES |
| HEVELAC.E.G...YLDP.LQL.AECFRCLRNACV.C.GNQDMIRDLDLIGTS.KL..LFQKLNVI.QES | |
| Retrocopy | HEVELACGEAGRPLYLDPQLQLTAECFRCLRNACVRCAGNQDMIRDLDLIGTSVKLVDLFQKLNVINQES |
| Parental | KLTAFRCGLQFLGNAVAGNEASQRILWKDAFPDLFLACLSYPDEKIVTYSCMILFTCLNSERLKDLQSRN |
| .LTAFRCGLQFLGNAVAGNEASQR.LWKDAFPDLFL.CLSY.DEKIVTYSCMILFTCLNSERLKDLQSRN | |
| Retrocopy | RLTAFRCGLQFLGNAVAGNEASQRMLWKDAFPDLFLGCLSYSDEKIVTYSCMILFTCLNSERLKDLQSRN |
| Parental | LTIALRVVEAYQKQADAEWAFLIISDYLLKIPELVNSLYAKLSHQERVTLLDLMIAKLVGDEPLTSEDIA |
| LT.ALRVV.AYQK.ADA.WAFLIIS.YLL..PELVNSLYAKLSHQERV.LLDLMIAKLVGDEPLTSE..A | |
| Retrocopy | LTVALRVVQAYQKLADADWAFLIISEYLLRSPELVNSLYAKLSHQERVALLDLMIAKLVGDEPLTSEFTA |
| Parental | AFLSHAGFVASKFQEKCKSVLKLASTGHSDDEEALTTIRLLHVLCEMSANCDLLPSLQAFPGLLKTAVET |
| AFLSH.GFVAS.FQEKCKSVLKLAS..HS.DEEALTTIRLLHVLCEMSANCDLLPSLQAFPGLL.TAVET | |
| Retrocopy | AFLSHTGFVASRFQEKCKSVLKLASSDHSGDEEALTTIRLLHVLCEMSANCDLLPSLQAFPGLLQTAVET |
| Parental | LKMTHLAGRQTLNVFTTSPCVRGDGDISSPVAGFKSYLIRLIGNLCYKDKNNQDKVYQLDGIPLILDSCS |
| L.MTHLAG.QT.NVFTTSPCVRG.GDISSPVAGFKS.LIRLIGNLCYKDKNNQDKVYQLDGIPLILDSCS | |
| Retrocopy | LQMTHLAGKQTPNVFTTSPCVRGEGDISSPVAGFKSHLIRLIGNLCYKDKNNQDKVYQLDGIPLILDSCS |
| Parental | IDDNNPFLNQWVVYAIRNLTEQNKRNQELIAKMENHGLADTAMLKKMGLEVEQQDRKLTLRSTRKASGGE |
| .DDNNPFL..W.VYAIRNLTEQNKRNQELIAKMENHGLADTAMLKKMGLEVEQ.D.KLT.RSTRKASGG. | |
| Retrocopy | MDDNNPFLKEWAVYAIRNLTEQNKRNQELIAKMENHGLADTAMLKKMGLEVEQRDGKLTVRSTRKASGGK |
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 | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1621 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1621 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000007304 | 1 retrocopy |
retro_mdom_1621 ,
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