RetrogeneDB ID:

retro_cjac_3317

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:9:76935487..76937194(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TLE1
Ensembl ID:ENSCJAG00000003424
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3317
ACAGAGAGCCGGGCACAAGTAATTCCCTCCTGGTCCCAGACAGATAAATGTAGAAATGAGCCAGAATTTTCCAATGACAT
CAAGAAAAGGAAGGTGGATGATAAGGACTCCAGCCATTATGACAGTGATGGTGACAAAAGAGACAACTAAGTTGTAGATG
TGTCTAATGAGGACCCACCTTCCCCATGAGCAAGCCCTGCCCACTCTCCCAGGGAAAATGGAATCGACAAGAACCGCCTG
CTAAAGAAGGATGCTTCTAGCAGGCCGGCTTCCACAGCCTCCTCATGAAGTTCCACGTCTTTGAAATCCAAAGAAATGAC
TTTGCATGAAAAAGCCAGCAGGCCTGTTCTGAAATCTAGCACACCAATGCCTCGGAGTGACATGCCAATGCCAGGCACCA
GCGCCACTTCAGGCCTCCGTCCAGGCCTCAGCAAGCCTTCAGCCATAGACCCCCTCATTAACCAAGCAGCAGCTGGCTTT
AGAACACCCCTGGCAGTGCCCAGCCCATACCCTGCTTCTTTTGGGATGGTCCCCCATGCTGGCTTGAACAGCGAGCTGAC
CAGCCCAGGTGCCGCCTCTGCCAGTTTACACAACATGTCACCCTAGATGAGTGCTGCAGCTGTCATGGCTGCCGTGGTGG
CCTATGGGCGCTCCCCCATGGTGGGGTTTGATCCTCCCCCTCACATGAGAGTATTTACCATTCCTCCAAAACTGGCAGGA
ATCCCCAGGGGAAAACCTGCATATTCCTTCCATGTTACTGCAGACGGTCAGTTGCAGCCTGTCCCTTTCCCCCCCAACGC
CTTCATCAGACCTGGAATCCCCCGGCACGCTCACCAGATCAACACCCTCAACCACAGGGACTTGGTGTGCACTGTGACCA
TCAGCAACCACACGACATAGGTGTACATGGGCGGGAAGGACTGCGTCAAGGTCTGGGACATCAGCCGCCCTGGCAATAAG
AGTCCTGTCTCCCAGCTCAACTGTCTGAATAGAGATAATGATATCTGTTCCTGTAAATTGCTACCTGATGGCTGCACTCT
TATAGTGGGAGGAGAAGCCAGTACTTTGTCCATTTGGGACCTGGCAGCTCTGACCCTGTGCATCAAGGCAGAGCTGACAT
CCTTGGCCCCTGCCTGCCACGCCCTGGCCATCAGCCCTGATTCCGAGGTCTGCTTCTCATGCTGCAGTGACAGCAGCATT
GCTGTGTGGGATCTGCACAACCAGATACTAGTGAGGCAATTCCAGAGCCACACAGATGGAGCCAGCTTTTCTAATGATGG
CACCAAGCTCTGGATGGGCGGTTTGGACAACACGGTCAGGTCCTGGGACCTGCGCAAGGGGCAGCAGCTGCAGCAGCACG
ACTTCACCTCCCAGATCTTCTCCCTGGGGTACTGCGTCACCAGGGAGTGGCTGGTGGTGGGTATGAAAAGCAGCAACGTG
TAGATGCTGCACATGAACAAGCCTGACAAGTACCAGCTGCACCTGCATGAGAGCTGCATGTTGTCCCTGAAATTTGCTTT
CTGCGGTAAATGGTTTGTGAGTACTGGAAAAGATAATCTCCTCAATGCTTGGCGGACCCCATATGGAGTCAGTATATTCC
AGTCCAAAGAGTACTCATCAGTGCCTAGCTGTGACATCTCTGTGGATGACAAGTACATAGTCACTGGCTCAGGGGACAAG
AAGGCTACGGTCTATGAAGTTATCTAC

ORF - retro_cjac_3317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.99 %
Parental protein coverage: 74.42 %
Number of stop codons detected: 6
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTSNSLLVPDSLRGTDKRRNGPEFSNDIKKRKVDDKDSSHYDSDGDKSDDNLVVDVSNEDPSSPRASPAHS
T.....V..S...TDK.RN.PEFSNDIKKRKVDDKDSSHYDSDGDK.D.N.VVDVSNEDP.SP.ASPAHS
RetrocopyTESRAQVIPSWSQTDKCRNEPEFSNDIKKRKVDDKDSSHYDSDGDKRD-N*VVDVSNEDPPSP*ASPAHS
ParentalPRENGIDKNRLLKKDASSSPASTASSGSSTSLKSKEMSLHEKASTPVLKSSTPTPRSDMPTPGTSATPGL
PRENGIDKNRLLKKDASS.PASTASS.SSTSLKSKEM.LHEKAS.PVLKSSTP.PRSDMP.PGTSAT.GL
RetrocopyPRENGIDKNRLLKKDASSRPASTASS*SSTSLKSKEMTLHEKASRPVLKSSTPMPRSDMPMPGTSATSGL
ParentalRPGLGKPPAIDPLVNQAAAGLRTPLAVPGPYPAPFGMVPHAGMNGELTSPGAAYASLHNMSPQMSAAAAA
RPGL.KP.AIDPL.NQAAAG.RTPLAVP.PYPA.FGMVPHAG.N.ELTSPGAA.ASLHNMSP.MSAAA..
RetrocopyRPGLSKPSAIDPLINQAAAGFRTPLAVPSPYPASFGMVPHAGLNSELTSPGAASASLHNMSP*MSAAAVM
ParentalAAVVAYGRSPMVGFDPPPHMRVPTIPPNLAGIPGGKPAYSFHVTADGQMQPVPFPPDALIGPGIPRHARQ
AAVVAYGRSPMVGFDPPPHMRV.TIPP.LAGIP.GKPAYSFHVTADGQ.QPVPFPP.A.I.PGIPRHA.Q
RetrocopyAAVVAYGRSPMVGFDPPPHMRVFTIPPKLAGIPRGKPAYSFHVTADGQLQPVPFPPNAFIRPGIPRHAHQ
ParentalINTLNHGEVVCAVTISNPTRHVYTGGKGCVKVWDISHPGNKSPVSQLDCLNRDNYIRSCKLLPDGCTLIV
INTLNH...VC.VTISN.T..VY.GGK.CVKVWDIS.PGNKSPVSQL.CLNRDN.I.SCKLLPDGCTLIV
RetrocopyINTLNHRDLVCTVTISNHTT*VYMGGKDCVKVWDISRPGNKSPVSQLNCLNRDNDICSCKLLPDGCTLIV
ParentalGGEASTLSIWDLAAPTPRIKAELTSSAPACYALAISPDSKVCFSCCSDGNIAVWDLHNQTLVRQFQGHTD
GGEASTLSIWDLAA.T..IKAELTS.APAC.ALAISPDS.VCFSCCSD..IAVWDLHNQ.LVRQFQ.HTD
RetrocopyGGEASTLSIWDLAALTLCIKAELTSLAPACHALAISPDSEVCFSCCSDSSIAVWDLHNQILVRQFQSHTD
ParentalGASCIDISNDGTKLWTGGLDNTVRSWDLREGRQLQQHDFTSQIFSLGYCPTGEWLAVGMESSNVEVLHVN
GAS....SNDGTKLW.GGLDNTVRSWDLR.G.QLQQHDFTSQIFSLGYC.T.EWL.VGM.SSNV..LH.N
RetrocopyGAS---FSNDGTKLWMGGLDNTVRSWDLRKGQQLQQHDFTSQIFSLGYCVTREWLVVGMKSSNV*MLHMN
ParentalKPDKYQLHLHESCVLSLKFAYCGKWFVSTGKDNLLNAWRTPYGASIFQSKESSSVLSCDISVDDKYIVTG
KPDKYQLHLHESC.LSLKFA.CGKWFVSTGKDNLLNAWRTPYG.SIFQSKE.SSV.SCDISVDDKYIVTG
RetrocopyKPDKYQLHLHESCMLSLKFAFCGKWFVSTGKDNLLNAWRTPYGVSIFQSKEYSSVPSCDISVDDKYIVTG
ParentalSGDKKATVYEVIY
SGDKKATVYEVIY
RetrocopySGDKKATVYEVIY

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
SRP051959_colon 0 .02 RPM 14 .13 RPM
SRP051959_heart 0 .18 RPM 5 .38 RPM
SRP051959_kidney 0 .00 RPM 6 .74 RPM
SRP051959_liver 0 .02 RPM 12 .67 RPM
SRP051959_lung 0 .15 RPM 15 .71 RPM
SRP051959_lymph_node 0 .02 RPM 20 .07 RPM
SRP051959_skeletal_muscle 0 .02 RPM 5 .35 RPM
SRP051959_spleen 0 .04 RPM 6 .01 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_3317 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3317 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3317 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
Callithrix jacchus ENSCJAG00000003424 1 retrocopy
retro_cjac_3317 ,


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