RetrogeneDB ID:

retro_cfam_1576

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:35:26167586..26169839(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000011738
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_1576
CTAGAACGGATCCTGTGCCTGCAGCAGTAGCAGCTGCAGCATATGCAGCTCACCGAACATTGGGCCCTCCACTCTGGTGT
GGCAGGAGTGGACACTCTCAAGACGCTGAGCAGACACATGTCCCAGCAGGTTTCCACAGCTGTGGCCTTGCTCAGCCAGA
AAGCTGGCAGCCAGGGCCTGTCTCTGGATGCCTTGAAACCGGCCAAACTACCTTGCGCAAACATCCCTTCCACCGTCAGC
TCTGTGGCCCAGGGGCTGGCACCTTTCACCCTGAAGCCCATATGACAAGGGTGCTGCTGAACATCATGTCGTGCCTTTCT
GGTGCTTTGCTACCTCAGGCCCCTGGCTCTGTGCTCTTCCAGAGCCCTTTCTCCACCATGGTGTTAGACCCATCCAAGAA
AGGGAAGGGGAAGCCGCCGAACATGTCCCCAGTGGAGGCCAAACCCAAAGATGAGGCCATCCTCTGCAAGCACAGGTGTA
AGTACTGTAGGAAGGTTTTGGGGACCAATAGCTTCCTACAGATCCACCTCACCTCCCATACCAGAGAGAGACCCTTTTTG
TGCTGTCTGTGGCCACTGGTTCACCACCAAGGGCAACCTCAAGGTGCACTTTCATTGACATCATCAGGTGAAGGCCAACC
CCCAGCTCTTTGCAGAGTTCCATGACAAAATGGCAACAGGCAATGACATTCCCTATGCAATCTCTGTACCCAGCCCTGTA
GATGAATTAAGTCTCTCTTTAGACAACAAACCTGTCCTTTTAAGAGGAATCCCCAGTCTAGGGCTATCTCAGAATTCTCT
CTTCAGGGACTAACCCCAAGTACCTAATGCACAACCCACTGCCCAATGACCTGCAGCCTAGGCCTTCCTGGGAAAGTAAG
GACCGACCCCTACTATCGAGGGGTGGTGGTGGAGGGGGTTGCAAACCACACTTCCCCAGCATTGGTGGCTTCCAAGGGAG
TAGGACCCCCAGCCAGGGTCAGAGACCCGAAATTACAAAAGCTGGTGGAGAACATTGACAAGGCCACTACTGATCCCAAC
AAATGTCTCATTTCCCACCATTCTTGAGATTCCAGAGCTCCCTCAAGATGCATTACTGCACCCACACCGGGGAGAGGCCA
TTTCATTGTAAGATCTGTGGTCAGGCCTTCTCCACCAAGGGCAACCTGAAGACACACCTCAGGATTCACCAGACCAACAT
GTCCATAAAGACACAGCAATCATGCGCCATCTGCCAGAAGAAGTTTATGAATGTGGTCCTGCTGCAGCAGCACATCCAGA
TGCACATAGATGGCCAGATTCCCATCACGCCTCTGCCTGAGAACCCCTATGATTTTACGGGTCCAGAGGCTGCGATGGTC
AGCGAAAATGGTAGCGCAGGTGCCACCTGTTATGATGACATCATTGAGAGCATCGATGTTGACTAGCTCAGCCACCCAGT
ACGCTTCTGGCAGCTCCCTGAAGGACCCCGTGCCTCTTCCCAACATCCACTCAGCATCACCCACTCTCCGGTTCTCCGTG
AAAGCTGCCCTAGATGCCCCAGGGAAGGTGGGTCCTGGTCCTCTTGTCTAGCAGCAGCAGAGCAGCAGAGAAAATGGTCC
ATTGGAGAGCGACAGCTTGACCAACAACTCACCGTCCTCGGTGATGGGAGACCAGGAGTACCAGAGCCGAAGTCCAGATG
TGCTGAAGACCACATCCTTCCAGGTCCTGTCCCTGGACAATAGCCACGCAGAGGGCATCCAGTCCGGGTCTCCTGATGCT
GGTGGCAAAGCAGACAGCTCCAAGAACAGCCACACTGAGATGGAAGGTCTAGAAGTCTGCCATCAACATTTATCCAAGCC
CAGCCAACCTATGTCAAAGTTGAAGTCCCTGGTGCGTTTGTTGGACTTGCGCCCATATCCGCAGGCATGACACCTTTGCT
AGTGGCCCAGCCATGCTAACAGGCCAAACAACACAGGTATACACGGTGTGAGAAGAATTTATCTAGGGGAGCGCTCTTCA
AATTCATGAGCAGACTCACACTGGGGAGAAGCCTTTTGTGTGTAACATATATGGGTGAGCTTTTACCACCAAAAGCAACT
TGAAGGTCCACTATATGACACATGGGGCGAACAATAGCTCAGCTCTCTGTGGGAGGAAACTGGCCATCAAGAACACCATG
GCTCTGTTAGGAACTGATGGGAAGAGAGTCCCTGAGATGTTTCCAAAGGAAATCCTGGCCCCTTTGGTGAACATGGACCC
TGTGGTATGGAAT

ORF - retro_cfam_1576 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.88 %
Parental protein coverage: 70.78 %
Number of stop codons detected: 6
Number of frameshifts detected 11


Retrocopy - Parental Gene Alignment:

ParentalLQQIQLTEQIRVQVNMWASH-ALHSGVAGADTLKTLGSHMSQQVSAAVALLSQKAGSQGLSLDALKPAKL
L..I....Q...Q......H.ALHSGVAG.DTLKTL..HMSQQVS.AVALLSQKAGSQGLSLDALKPAKL
RetrocopyLERILCLQQ*QLQHMQLTEHWALHSGVAGVDTLKTLSRHMSQQVSTAVALLSQKAGSQGLSLDALKPAKL
ParentalPHANIPSTASS--QGLASFALKP-DGTRVLPNVMSRLPGALLPQAPGSVLFQSPFSTVALDPSKKGKGKP
P.ANIPST.SS..QGLA.F.LKP...TRVL.N.MS.L.GALLPQAPGSVLFQSPFST..LDPSKKGKGKP
RetrocopyPCANIPSTVSSVAQGLAPFTLKP<HMTRVLLNIMSCLSGALLPQAPGSVLFQSPFSTMVLDPSKKGKGKP
ParentalPNVSPVEAKPKDEAILCKHKCKYCSKVFGTDSSLQIHLRSHTGER-PFVCSVCGHRFTTKGNLKVHFHRH
PN.SPVEAKPKDEAILCKH.CKYC.KV.GT.S.LQIHL.SHT.ER.PF.C.VCGH.FTTKGNLKVHFH.H
RetrocopyPNMSPVEAKPKDEAILCKHRCKYCRKVLGTNSFLQIHLTSHTRER>PF-CAVCGHWFTTKGNLKVHFH*H
ParentalPQVKANPQLFAEFHDKMTAGNGIPYALSVPVPVDESSLSLDSKPVLVTGTPGLGLPQN-LSSGTNPKDLL
.QVKANPQLFAEFHDKM..GN.IPYA.SVP.PVDE.SLSLD.KPVL..G.P.LGL.QN.LSSGTNPK.L.
RetrocopyHQVKANPQLFAEFHDKMATGNDIPYAISVPSPVDELSLSLDNKPVLLRGIPSLGLSQN>LSSGTNPKYLM
ParentalGGPLPNDLQPGPSPESEDGSLLS----GGG-PNHTSPR-VGGFQGSGTP-EPGSETL-KLQQLVENIDKA
..PLPNDLQP.PS.ES.D..LLS....GGG..NHTSP...GGFQGS.TP..PGSET..KLQ.LVENIDKA
RetrocopyHNPLPNDLQPRPSWESKDRPLLSRGGGGGG>ANHTSPA<IGGFQGSRTP<QPGSETR<KLQKLVENIDKA
ParentalTTDPNECLICHR-VLSCQSSLKMHYRTHTGERPFQCKICGRAFSTKGNLKTHLGVHRTNTSIKTQHSCPI
TTDPN.CLI.H...L..QSSLKMHY.THTGERPF.CKICG.AFSTKGNLKTHL..H.TN.SIKTQ.SC.I
RetrocopyTTDPNKCLISHH<FLRFQSSLKMHYCTHTGERPFHCKICGQAFSTKGNLKTHLRIHQTNMSIKTQQSCAI
ParentalCQKKFTNAVLLQQHIRMHMGGQIPNTPLPENPCDFAGPEAAMVSENGSAGATCHDDVIESIDVDEL-GPQ
CQKKF.N.VLLQQHI.MH..GQIP.TPLPENP.DF.GPEAAMVSENGSAGATC.DD.IESIDVD.L...Q
RetrocopyCQKKFMNVVLLQQHIQMHIDGQIPITPLPENPYDFTGPEAAMVSENGSAGATCYDDIIESIDVD*L>ATQ
ParentalDASGSSLKVPVPLPSVHSASPTLGFAVTAALDAPGKVGPAPLVLQRQSSRENGSVESDGLTNDSSSSVMG
.ASGSSLK.PVPLP..HSASPTL.F.V.AALDAPGKVGP.PLV.Q.QSSRENG..ESD.LTN.S.SSVMG
RetrocopyYASGSSLKDPVPLPNIHSASPTLRFSVKAALDAPGKVGPGPLV*QQQSSRENGPLESDSLTNNSPSSVMG
ParentalDQEYQSRSPDVLETASFQALSPANSQAESIKSRSPDAGGKADSSENSRTEMEG-RSSLPSTFIRTQPTYV
DQEYQSRSPDVL.T.SFQ.LS..NS.AE.I.S.SPDAGGKADSS.NS.TEMEG...SLPSTFI..QPTYV
RetrocopyDQEYQSRSPDVLKTTSFQVLSLDNSHAEGIQSGSPDAGGKADSSKNSHTEMEG<SRSLPSTFIQAQPTYV
ParentalKVEVPGAFVGPATMSPGMTPLLTAQPRRQAKQHGCTRCGKNFSS-ASALQIHERTHTGEKPFVCNICGRA
KVEVPGAFVG.A..S.GMTPLL.AQP..QAKQH..TRC.KN.S...SALQIHE.THTGEKPFVCNI.G.A
RetrocopyKVEVPGAFVGLAPISAGMTPLLVAQPC*QAKQHRYTRCEKNLSR<GSALQIHEQTHTGEKPFVCNIYG*A
ParentalFTTKGNLKVHYMTHGANNSSARRGRKLAIENTMALLGTDGKRVPEMFPKEILAPSVNMDPVVWN
FTTK.NLKVHYMTHGANNSSA..GRKLAI.NTMALLGTDGKRVPEMFPKEILAP.VNMDPVVWN
RetrocopyFTTKSNLKVHYMTHGANNSSALCGRKLAIKNTMALLGTDGKRVPEMFPKEILAPLVNMDPVVWN

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
SRP012049_cerebellum 0 .17 RPM 0 .00 RPM
SRP017611_brain 0 .08 RPM 0 .08 RPM
SRP017611_kidney 0 .00 RPM 1 .06 RPM
SRP017611_liver 0 .00 RPM 0 .51 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1576 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1576 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1576 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
Canis familiaris ENSCAFG00000011738 1 retrocopy
retro_cfam_1576 ,


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