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:

ParentalYSKVLCIAFEVLQGLQYMNKHGIVHRALSPHNILLDLKGHVKLAKFGLYHMTAHGDDVDFPIGYPSYLAP
YSKVLCIAFEVLQGLQYMNKHGIVH..LSPHN.LLD.KGHVKLAKFGLYHMTAHG.DVDFPIGY.SYL..
RetrocopyYSKVLCIAFEVLQGLQYMNKHGIVHCTLSPHNVLLDRKGHVKLAKFGLYHMTAHGVDVDFPIGYLSYLVH
ParentalEVIAQGISKTTDHVPNGKPLPSGPKSDVWSLGIILFELCMGRKLFQSLDISERL-KFLLTLDCVDDTVIV
EVIAQGISKTTDHVPNGKPLPSGPKSDVWSLGIILFELCMGRKLFQSL.ISER..KFLLTL.CVDDT.IV
RetrocopyEVIAQGISKTTDHVPNGKPLPSGPKSDVWSLGIILFELCMGRKLFQSLEISERV<KFLLTLACVDDTIIV
ParentalLAEEHGCLDVVKELPENVMGLLKRCLTFHPSNRPTPSELMQDKVFSEVSPSYTPFTKPASLF-SSSLRCA
L.EEHGCLD.VKEL..NVM.LLKRCLTFH.SNRPTP.ELMQDK.FSE.SP.YTPFTKPASLF.SSSLRCA
RetrocopyLVEEHGCLDIVKELSQNVMDLLKRCLTFHASNRPTPGELMQDKIFSEMSPLYTPFTKPASLF<SSSLRCA
ParentalDLTLPEDISQLCQDINSDYLAERSIEEVYYLWCLAGGDLEKELVNKEIIRSKPPVCTLPNFLFEDGESFG
.LT.PEDISQLCQDINSD.L.ERSIEEVYYL..LAGGDLEKE.VNKEIIRSKPPVCTLPNFLFEDGESFG
RetrocopyYLTSPEDISQLCQDINSDNLVERSIEEVYYL*YLAGGDLEKEQVNKEIIRSKPPVCTLPNFLFEDGESFG
ParentalQGRDRSSLLDDTTVTLSLCQLRNRLKDVGGEAFYPLLEDDQSNLPHSNSNNELSAAATLPLIIRERDTEY
QGRDRSSLLDDTTVTLSLCQLRNRLKDV.GEAFYPLLEDDQSNLPHSNSNNE.SAAATLPLIIRERDTEY
RetrocopyQGRDRSSLLDDTTVTLSLCQLRNRLKDVDGEAFYPLLEDDQSNLPHSNSNNEVSAAATLPLIIRERDTEY
ParentalQLHRIVLFDRLLKAYPYKKN-QIWKEARVDIPPLMRGLTWAALLGVEGAIHAKYDAIDKDTPIPTDRQIE
.LHRIVLF.RLLKAYPY....QIWKEARVDIPPLMRGLTWAALLGVEGAIHA.YDAIDKDT..PTDRQIE
Retrocopy*LHRIVLFQRLLKAYPYXXX>QIWKEARVDIPPLMRGLTWAALLGVEGAIHAEYDAIDKDTSVPTDRQIE
ParentalVDIPRCHQYDELLSSPEGHAKFRRVLKAWVVSHPDLVYWQGLDSLCAPFLYLNFNNEALAYACMSAFIPK
VDIPRCHQYDELL.SPEGHAKFR.VL.AWV..HPDLVYW.GLDS.C.P.LYLNFN.EALAYAC.SAFIPK
RetrocopyVDIPRCHQYDELL*SPEGHAKFRCVLTAWVLPHPDLVYWKGLDSVCTP*LYLNFNKEALAYACVSAFIPK
ParentalYLYNFFLKDNSHVIQEYLAVFSQMIAFHDPELSNHLNEIGFIPDLYAIPWFLTMFTHVFPLHKIFHLWDT
YLYNF.LKDNSHVIQ.YLAVFSQMIAFHDPELSNHLNE.GFIPDLYAIPWFL..FTHVFPLHKIFHLWDT
RetrocopyYLYNF-LKDNSHVIQVYLAVFSQMIAFHDPELSNHLNEMGFIPDLYAIPWFLITFTHVFPLHKIFHLWDT
ParentalLLLGNSSFPFCIGVAILQQLRDRLLANGFNECILLFSDLPEIDIERCVRESINLFCWTPKSATYRQHAQP
LLLGNSSFPFCIGVAILQQLRDRLLANGF.ECILLFSDLPEID.E.CV.ESINLFCWTPKSAT.RQHAQP
RetrocopyLLLGNSSFPFCIGVAILQQLRDRLLANGFSECILLFSDLPEIDTECCV*ESINLFCWTPKSATNRQHAQP
ParentalPRPTSDGSGARSSTPYFSTECADPPKTDLSRESIPLNDLKSEVSPRISAEDLIDLCELTVTGHFKTPTKK
PRPTS.GSGAR.STPYFSTECA.PPKTDLSRESIPLNDLKSEVS..ISAEDLIDLCELTVTGHFKTPTKK
RetrocopyPRPTSEGSGARNSTPYFSTECAGPPKTDLSRESIPLNDLKSEVSLWISAEDLIDLCELTVTGHFKTPTKK
ParentalTKPSKPKLLVVDIRNTEEY
TK.SKPK.LVVDIRNTEE.
RetrocopyTKSSKPKFLVVDIRNTEEF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_272 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

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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