RetrogeneDB ID: | retro_ecab_272 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 12:13514891..13517035(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TBCK | ||
| Ensembl ID: | ENSECAG00000006577 | ||
| Aliases: | None | ||
| Description: | TBC1 domain containing kinase [Source:HGNC Symbol;Acc:28261] |
Retrocopy-Parental alignment summary:
>retro_ecab_272
TATTCAAAGGTTTTGTGTATAGCGTTTGAGGTACTTCAGGGCTTGCAGTATATGAACAAACATGGTATAGTGCACTGTAC
ACTGTCTCCTCATAATGTCCTTTTGGACCGAAAGGGACATGTTAAATTGGCTAAATTTGGACTTTATCACATGACAGCTC
ATGGTGTCGATGTTGATTTCCCAATTGGGTATCTGTCCTACTTGGTGCATGAGGTAATTGCACAAGGGATTTCCAAAACG
ACTGATCATGTGCCAAATGGAAAACCATTGCCTTCTGGCCCGAAATCAGATGTATGGTCTCTTGGAATCATTTTATTTGA
GCTTTGCATGGGAAGAAAGTTATTTCAGAGCTTGGAGATTTCTGAAAGAGTAAATTTTTGCTTACATTGGCCTGTGTGGA
TGATACTATAATAGTTCTGGTTGAAGAGCATGGTTGTCTGGACATTGTAAAGGAGCTTTCTCAAAATGTGATGGATCTTT
TGAAGAGGTGCCTCACCTTTCACGCTTCCAACAGGCCAACCCCAGGTGAATTAATGCAGGACAAGATATTCAGTGAAATG
TCACCTTTATACACCCCCTTTACCAAACCTGCCAGTCTGTTTCATCTTCTCTGAGATGTGCTTATTTAACTTCACCTGAG
GATATCAGTCAGCTGTGTCAAGACATAAACAGTGATAACCTGGTGGAAAGATCTATTGAAGAAGTGTATTACCTTTAATA
TTTAGCTGGAGGTGACTTGGAGAAAGAGCAGGTCAACAAGGAGATCATTCGGTCCAAGCCACCTGTCTGCACACTTCCCA
ATTTTCTCTTTGAAGATGGTGAAAGCTTTGGACAAGGTCGAGATAGAAGCTCATTATTAGATGACACCACTGTGACATTG
TCATTATGCCAGCTAAGAAATAGATTAAAAGATGTTGATGGAGAAGCATTTTACCCGTTACTCGAAGATGACCAGTCTAA
TTTGCCCCATTCAAACAGCAATAACGAGGTGTCTGCAGCTGCCACTCTCCCTTTAATCATCCGAGAGAGGGACACAGAGT
ACTAACTTCACAGAATCGTTCTCTTTCAAAGGCTGCTAAAGGCGTATCCATATAAAAAAAAATCAGATCTGGAAAGAAGC
AAGAGTTGACATTCCTCCTCTAATGAGAGGTTTAACCTGGGCTGCTCTTCTGGGAGTTGAGGGGGCTATTCATGCAGAGT
ATGATGCAATTGATAAAGATACTTCAGTTCCTACAGATAGACAAATTGAAGTGGATATTCCTCGTTGTCATCAGTATGAT
GAACTCTTATAATCACCAGAAGGTCATGCAAAGTTTAGATGTGTACTAACAGCCTGGGTGTTGCCCCATCCTGATCTCGT
GTATTGGAAAGGTCTTGACTCAGTTTGTACTCCATAACTATATTTAAATTTCAATAAGGAAGCCCTAGCTTATGCGTGTG
TGTCCGCCTTTATCCCCAAATACCTGTATAATTTCTTGAAAGACAACTCACATGTAATACAAGTGTATTTGGCTGTGTTC
TCTCAGATGATTGCATTCCATGATCCGGAGCTGAGCAATCATCTCAATGAGATGGGGTTTATTCCAGATCTATATGCCAT
CCCTTGGTTTCTCATCACGTTTACTCATGTATTTCCACTGCACAAAATTTTCCACCTCTGGGATACCTTACTACTTGGGA
ATTCCTCTTTCCCATTCTGTATTGGAGTAGCAATTCTTCAGCAGCTACGGGACCGGCTTTTGGCTAATGGCTTTAGTGAG
TGCATTCTTCTCTTCTCTGATTTACCAGAAATTGACACTGAATGCTGTGTATGAGAATCAATCAATCTATTTTGTTGGAC
TCCTAAAAGTGCTACTAACAGACAGCATGCTCAGCCTCCAAGGCCGACTTCTGAGGGCAGTGGAGCCAGAAATTCGACTC
CTTATTTCTCCACTGAGTGTGCAGGACCTCCAAAAACAGATCTGTCAAGAGAGTCCATCCCATTAAATGACCTAAAATCC
GAAGTATCCCTGTGGATTTCAGCAGAGGACCTGATTGACTTGTGCGAGCTCACGGTGACAGGCCACTTCAAAACACCCAC
CAAGAAAACAAAGTCCAGTAAACCAAAGTTCCTGGTCGTGGACATTCGGAATACTGAAGAATTC
ORF - retro_ecab_272 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.13 % |
| Parental protein coverage: | 88.94 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | YSKVLCIAFEVLQGLQYMNKHGIVHRALSPHNILLDLKGHVKLAKFGLYHMTAHGDDVDFPIGYPSYLAP |
| YSKVLCIAFEVLQGLQYMNKHGIVH..LSPHN.LLD.KGHVKLAKFGLYHMTAHG.DVDFPIGY.SYL.. | |
| Retrocopy | YSKVLCIAFEVLQGLQYMNKHGIVHCTLSPHNVLLDRKGHVKLAKFGLYHMTAHGVDVDFPIGYLSYLVH |
| Parental | EVIAQGISKTTDHVPNGKPLPSGPKSDVWSLGIILFELCMGRKLFQSLDISERL-KFLLTLDCVDDTVIV |
| EVIAQGISKTTDHVPNGKPLPSGPKSDVWSLGIILFELCMGRKLFQSL.ISER..KFLLTL.CVDDT.IV | |
| Retrocopy | EVIAQGISKTTDHVPNGKPLPSGPKSDVWSLGIILFELCMGRKLFQSLEISERV<KFLLTLACVDDTIIV |
| Parental | LAEEHGCLDVVKELPENVMGLLKRCLTFHPSNRPTPSELMQDKVFSEVSPSYTPFTKPASLF-SSSLRCA |
| L.EEHGCLD.VKEL..NVM.LLKRCLTFH.SNRPTP.ELMQDK.FSE.SP.YTPFTKPASLF.SSSLRCA | |
| Retrocopy | LVEEHGCLDIVKELSQNVMDLLKRCLTFHASNRPTPGELMQDKIFSEMSPLYTPFTKPASLF<SSSLRCA |
| Parental | DLTLPEDISQLCQDINSDYLAERSIEEVYYLWCLAGGDLEKELVNKEIIRSKPPVCTLPNFLFEDGESFG |
| .LT.PEDISQLCQDINSD.L.ERSIEEVYYL..LAGGDLEKE.VNKEIIRSKPPVCTLPNFLFEDGESFG | |
| Retrocopy | YLTSPEDISQLCQDINSDNLVERSIEEVYYL*YLAGGDLEKEQVNKEIIRSKPPVCTLPNFLFEDGESFG |
| Parental | QGRDRSSLLDDTTVTLSLCQLRNRLKDVGGEAFYPLLEDDQSNLPHSNSNNELSAAATLPLIIRERDTEY |
| QGRDRSSLLDDTTVTLSLCQLRNRLKDV.GEAFYPLLEDDQSNLPHSNSNNE.SAAATLPLIIRERDTEY | |
| Retrocopy | QGRDRSSLLDDTTVTLSLCQLRNRLKDVDGEAFYPLLEDDQSNLPHSNSNNEVSAAATLPLIIRERDTEY |
| Parental | QLHRIVLFDRLLKAYPYKKN-QIWKEARVDIPPLMRGLTWAALLGVEGAIHAKYDAIDKDTPIPTDRQIE |
| .LHRIVLF.RLLKAYPY....QIWKEARVDIPPLMRGLTWAALLGVEGAIHA.YDAIDKDT..PTDRQIE | |
| Retrocopy | *LHRIVLFQRLLKAYPYXXX>QIWKEARVDIPPLMRGLTWAALLGVEGAIHAEYDAIDKDTSVPTDRQIE |
| Parental | VDIPRCHQYDELLSSPEGHAKFRRVLKAWVVSHPDLVYWQGLDSLCAPFLYLNFNNEALAYACMSAFIPK |
| VDIPRCHQYDELL.SPEGHAKFR.VL.AWV..HPDLVYW.GLDS.C.P.LYLNFN.EALAYAC.SAFIPK | |
| Retrocopy | VDIPRCHQYDELL*SPEGHAKFRCVLTAWVLPHPDLVYWKGLDSVCTP*LYLNFNKEALAYACVSAFIPK |
| Parental | YLYNFFLKDNSHVIQEYLAVFSQMIAFHDPELSNHLNEIGFIPDLYAIPWFLTMFTHVFPLHKIFHLWDT |
| YLYNF.LKDNSHVIQ.YLAVFSQMIAFHDPELSNHLNE.GFIPDLYAIPWFL..FTHVFPLHKIFHLWDT | |
| Retrocopy | YLYNF-LKDNSHVIQVYLAVFSQMIAFHDPELSNHLNEMGFIPDLYAIPWFLITFTHVFPLHKIFHLWDT |
| Parental | LLLGNSSFPFCIGVAILQQLRDRLLANGFNECILLFSDLPEIDIERCVRESINLFCWTPKSATYRQHAQP |
| LLLGNSSFPFCIGVAILQQLRDRLLANGF.ECILLFSDLPEID.E.CV.ESINLFCWTPKSAT.RQHAQP | |
| Retrocopy | LLLGNSSFPFCIGVAILQQLRDRLLANGFSECILLFSDLPEIDTECCV*ESINLFCWTPKSATNRQHAQP |
| Parental | PRPTSDGSGARSSTPYFSTECADPPKTDLSRESIPLNDLKSEVSPRISAEDLIDLCELTVTGHFKTPTKK |
| PRPTS.GSGAR.STPYFSTECA.PPKTDLSRESIPLNDLKSEVS..ISAEDLIDLCELTVTGHFKTPTKK | |
| Retrocopy | PRPTSEGSGARNSTPYFSTECAGPPKTDLSRESIPLNDLKSEVSLWISAEDLIDLCELTVTGHFKTPTKK |
| Parental | TKPSKPKLLVVDIRNTEEY |
| TK.SKPK.LVVDIRNTEE. | |
| Retrocopy | TKSSKPKFLVVDIRNTEEF |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .00 RPM | 5 .78 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 11 .48 RPM |
| SRP021940_embryo | 0 .00 RPM | 16 .16 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 8 .13 RPM |
| SRP021940_synovial_membrane | 0 .03 RPM | 8 .98 RPM |
| SRP021940_testis | 0 .00 RPM | 7 .80 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_272 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_272 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_272 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000006577 | 1 retrocopy |
retro_ecab_272 ,
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