RetrogeneDB ID: | retro_mdom_1274 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:212533964..212535350(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HARS2 | ||
| Ensembl ID: | ENSMODG00000011309 | ||
| Aliases: | None | ||
| Description: | histidyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:4817] |
Retrocopy-Parental alignment summary:
>retro_mdom_1274
AGGATGAAGACTCAGCTGGAATTAAATAAAGAGAAACCCAGTTTTGTTATCAAGACTCCCAAGGGTACCAGAGATCTTAG
CCCTCAAAAGATGGCTATTGGAGAGAAAATCCTTAATGCTGTCATCAATTGTTTCAAGTGCCATGGAGCTAAAGGAATAG
ACACTCTAGTGTTTAAACTAAAGGAAATATTAACAGAGAAGTATGGAGAAGAATACAGGCTCATCTCTGATATGAAGGAT
CAGGGTGGGGAGCTGCTAGCTCTTCAATATGACCTCACAGTTCCTTTTGCTCATTATCTGGCCATGAATAAGATAAAGAA
GATGAAATGCTATCACATTGGGAAGGTTTAGTGAAGGGAGAGTCCCTCCATAATTCAAGGTCGATATCAGGAGTTTTGCC
AAGGTGATTTTGACATTGCAGGGCAATTTAATCCCATGATCCCTGATGCAGAGTGATTAAAGATCATACATGAAATTCTC
AACACATTAAAATTGGGAGACTTCCTAATTAAGGTGAATGACAGGAGAGTTGTGGATGGTATGTTTGCTGTCTGTGGTGT
CCCTGATAACAAATTTCATTTTATTTGTGCTTCAGTTGATAAGCTTGGCAAGATGTCCTGGAAGGATGTGAGACAAGAGA
TGACAGGAAAGATGGGACTCACCCCTAATATAGCAAATCTAATTGGGGTGTGGTGTGGTGGAGTGTCCCTAGTAGAGCAG
CTACTACAGGATCCCAAACTCTCACAGAACAAACAGGCTCTGGAAGGATTAAAGGACCTGAAACTTCTGTTTGAGTATCT
GACCCTGTTTGGTATTGCAGAGAAGATTTCCTTCGACTTGAGCCTGGCTTGAGGCCTGAGCTATTACCCAGGAGTGATCT
ATGAAGCAGTGATTCTTCAGAGCCCAGCCCAATAGGGGGAGGAAGCACTTGGTGTGGGCAGTGTGGCTTCTGGAGGGTGC
TATGATGGACTTCTTGGCATATTTGACCCCAAGGGTCGCAAGGTGCCCTGTGTGTGGCTCAGCATTGGGTTTGAAAGGAT
CTTCTCCATTGTGGAACAAAGGATGGAGGCCACTAAGAAAATACAAACAACAGAGACAGAGGTCCTTGTGGCTACAGCAC
AAAAGAATTTTCTTAGGGAACTAATAAAACTGATTGTAGAGCTCTGGGATGCTGGGATCAGGGCTGAGATGTTATATAAG
AAGAATCCCAGTTTCCTGACTCAGCTACATTAATGTGAGGAGACAGGCATCCCATTGGTGGCTATCATTGGAGAACAAGA
GCTAAAGGATGGTGTCATTAAGCTTCCTTCTGTGGCTAGTAGGAAAGAGGTAGACATTAAACGGGAAGATATTGTAACCA
AAAGCCAGAGAAGAATGTCTGAATCC
ORF - retro_mdom_1274 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.6 % |
| Parental protein coverage: | 91.9 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QMKTQLELNKEKSSFVIKTPKGTRDLSPQQMAIREKILNAVINCFKCHGAKGIDTPVFELKEILTEKYGE |
| .MKTQLELNKEK.SFVIKTPKGTRDLSPQ.MAI.EKILNAVINCFKCHGAKGIDT.VF.LKEILTEKYGE | |
| Retrocopy | RMKTQLELNKEKPSFVIKTPKGTRDLSPQKMAIGEKILNAVINCFKCHGAKGIDTLVFKLKEILTEKYGE |
| Parental | ESRLIYELKDQGGELLALRYDLTVPFARYLAMNKIKKMKRYHVGKVWRRESPSIIQGRYREFCQCDFDIA |
| E.RLI...KDQGGELLAL.YDLTVPFA.YLAMNKIKKMK.YH.GKV..RESPSIIQGRY.EFCQ.DFDIA | |
| Retrocopy | EYRLISDMKDQGGELLALQYDLTVPFAHYLAMNKIKKMKCYHIGKV**RESPSIIQGRYQEFCQGDFDIA |
| Parental | GQFDPMIPDAECLKIIHEILSTLQLGDFLIKVNDRRVVDGMFAVCGVPDNKFRFICASVDKLGKMSWKDV |
| GQF.PMIPDAE.LKIIHEIL.TL.LGDFLIKVNDRRVVDGMFAVCGVPDNKF.FICASVDKLGKMSWKDV | |
| Retrocopy | GQFNPMIPDAE*LKIIHEILNTLKLGDFLIKVNDRRVVDGMFAVCGVPDNKFHFICASVDKLGKMSWKDV |
| Parental | RQEMTGKIGLTPDVADQIGDYIQQCGGVSLVEQLLQDPKLSQNKQALEGLKDLKLLFEYLTLFGIAEKIS |
| RQEMTGK.GLTP..A..IG.....CGGVSLVEQLLQDPKLSQNKQALEGLKDLKLLFEYLTLFGIAEKIS | |
| Retrocopy | RQEMTGKMGLTPNIANLIGVW---CGGVSLVEQLLQDPKLSQNKQALEGLKDLKLLFEYLTLFGIAEKIS |
| Parental | FDLSLARGLDYYTGVIYEAVLLQSPTQQGEEALGVGSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERI |
| FDLSLA.GL.YY.GVIYEAV.LQSP.Q.GEEALGVGSVA.GG.YDGL.G.FDPKGRKVPCV.LSIG.ERI | |
| Retrocopy | FDLSLA*GLSYYPGVIYEAVILQSPAQ*GEEALGVGSVASGGCYDGLLGIFDPKGRKVPCVWLSIGFERI |
| Parental | FSIVEQRMEATKKIQTTETQVLVATAQKNFLRERMKLIAELWDAGIRAEMLYKKNPSFLTQLHYCEETGI |
| FSIVEQRMEATKKIQTTET.VLVATAQKNFLRE..KLI.ELWDAGIRAEMLYKKNPSFLTQLH.CEETGI | |
| Retrocopy | FSIVEQRMEATKKIQTTETEVLVATAQKNFLRELIKLIVELWDAGIRAEMLYKKNPSFLTQLH*CEETGI |
| Parental | PLVAIIGEQELKDGVIKLRSVASRKEVDIKREDIVTEIQRRMSES |
| PLVAIIGEQELKDGVIKL.SVASRKEVDIKREDIVT..QRRMSES | |
| Retrocopy | PLVAIIGEQELKDGVIKLPSVASRKEVDIKREDIVTKSQRRMSES |
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 | 126 .35 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 170 .41 RPM |
| SRP007412_heart | 0 .00 RPM | 106 .85 RPM |
| SRP007412_kidney | 0 .00 RPM | 169 .87 RPM |
| SRP007412_liver | 0 .00 RPM | 77 .54 RPM |
| SRP007412_testis | 0 .00 RPM | 88 .20 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1274 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1274 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 | ENSMODG00000011309 | 1 retrocopy |
retro_mdom_1274 ,
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