RetrogeneDB ID:

retro_cjac_1763

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:15753490..15755389(+)
Located in intron of:ENSCJAG00000018360
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLA
Ensembl ID:ENSCJAG00000006512
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1763
ATGCCGTTTCCCGTGACAACTCAGGGAACACCGCAGCCGGCGAAGCGCTATGGCATCTCCGCGCCGATCAGCTTAGCGGT
CCCCAAGGAGACGGACTGCCTCCTCACCCAGAGGCTAATAGAAACCCTCAGGCCCTTCGGGGTCTTCGAAGAGGAAGAGG
AACTGCAGCGCAGGATTTTAGTTTTGGAAAAATTAAATAATCTGGTAAAGGAATGGATACGCGAAATCAGTGAAAGCAAG
AGTCTTCCGCAATCTATACTTGAAAACGTTGGAGGAAAGATTTTTACATTTGGCTCCTACAGATTAGGAGTACATACGAA
AGGCGCAGATATTGACGCCTTGTGCATTGCACCAAGGCATGTGGATCGAAGTGACTTCTTCACCTCCTTCTATGCTAAGC
TGAAACTACAGGAGGAAGTAAAAGATTTAAGGGCTGTCGAGGAGGCATTTGTGCCAGTTATCAAATTGTGTTTTGATGGG
ATAGAGATTGATATTTTGTTTGCAAGATTAGCACTACAGACTATTCCAGAAGACTTGGACCTAAGAGATGACAGTCTACT
TAAAGATTTAGACATTAGAAGCATAAGAAGCCTCAACGGTTGCCGGGTAACTGATGAAATTTTACATCTAGTGCCAAACA
TTGACAACTTCAGGTTGACTCTGAGAGCCATCAAATTGTGGGCCAAATGCCACAGTATCTATTCCAATATACTAGGTTTC
CTCGGAGGTGTTTCCTGGGCCATGCTAGTAGCAAGAACTTGTCAGCTTTATCCAAATGCAGTAGCGTCAACTCTTGTACG
GAAGTTCTTCTTGGTATTTTCTGAATGGGAATGGCCAAATCCAGTGTTACTGAAAGAGCCTGAAGAACAGAATCTTAATT
TGCCAGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCTATCATCACACCAGCATACCCACAGCAG
AACTCCACATACAACGTGTCTGTTTCAACTAGGATGGTCATGATTGAAGAGTTTAAACAGGGGCTTGCTATCACACATGA
AATTTTGCTGAATAAGGCAGAGTGGTCCAAACTCTTTGAAGCTCCAAGCTTCTTTCAAAAGTACAAGCATTATATTGTAC
TTCTGGCAAGTGCACCAACAGAAAAACAACATTTAGAATGGGTGGGCTTGGTGGAATCAAAGATCCGGATCCTGGTTGGG
AGCTTGGAGAAGAATGAATTTATTACACTGGCACATGTGAATCCACAGTCATTTCTAGCACCCAAAGAAAATCCTGGTAA
GAAAGAATTTCGTACAATGTGGGTGATTGGGTTAGTGCTAAAGAAGCCAGAAAACTCTGAAATTCTCAGTATTGATCTCA
CCTATGATATCCAGTCTTTCACAGATACTGTTTATAGGCAAGCAGTGAATAGTAAGATGTTTGAGACGGGCATGAAAATT
GCTGCAATGCATTTAAGAAGAAAGGAACTTCATCAGCTGCTGCCTCATCATGTGCTTCAGGAAAAGAAAGCACACTCTCC
AGAAGGTAGAAGATTGACAGATTTGAATGACAGAAGCTTTGACTTGTCTGCAGGTGGTGAAAACAGCATTTCTGTGCCTT
CATCTACTAGCACTATGAAGACAGGCCCATTGATTAGCAGTTCTCAGGGTAGAAACAGTCCTGCCCTGGCTGTAATGACA
GCATCTGTGACGAACATACGGGCTACTGAAATTTCCTTGCAACAGGTGAATACCAGTGAAAGTTCAGGGGCTGCATTAAA
CGAAAGTATTCCTCATGCTGTCTCTCAGCCTGCCATTGCTCCATCACCAAAGCCCATGGTCACCAGAGTTGTTTCTTCGA
CATGTCTCATAAGCCATCCAGACCTTCAGGAAACGCAGCAACAAACATATCGAATCCTA

ORF - retro_cjac_1763 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.64 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILILGKLNN
MPFPVTTQG..Q...P.K.YGI..PISLA.PKETDC.LTQ.LIETL.PFGVFEEEEELQRRIL.L.KLNN
RetrocopyMPFPVTTQGTPQ---PAKRYGISAPISLAVPKETDCLLTQRLIETLRPFGVFEEEEELQRRILVLEKLNN
ParentalLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQ
LVKEWIREISESK.LPQS..ENVGGKIFTFGSYRLGVHTKGADIDALC.APRHVDRSDFFTSFY.KLKLQ
RetrocopyLVKEWIREISESKSLPQSILENVGGKIFTFGSYRLGVHTKGADIDALCIAPRHVDRSDFFTSFYAKLKLQ
ParentalEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLK.LDIR.IRSLNGCRVTDEI
RetrocopyEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKDLDIRSIRSLNGCRVTDEI
ParentalLHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
LHLVPNIDNFRLTLRAIKLWAK.H.IYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WE
RetrocopyLHLVPNIDNFRLTLRAIKLWAKCHSIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWE
ParentalWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDE
WPNPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.E
RetrocopyWPNPVLLKEPEEQNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHE
ParentalILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
ILL.KAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
RetrocopyILLNKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
ParentalFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKR
F.APKENP.K.EFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQA.NSKMFE..MKIAAMH..R
RetrocopyFLAPKENPGKKEFRTMWVIGLVLKKPENSEILSIDLTYDIQSFTDTVYRQAVNSKMFETGMKIAAMHLRR
ParentalKQLHQLLPNHVLQKKKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLSSSGSSQGRNSPA
K.LHQLLP.HVLQ.KK.HS.EG..LT.LND.S.DLS....NS.SVPS.TS..KT.PL.S..SSQGRNSPA
RetrocopyKELHQLLPHHVLQEKKAHSPEGRRLTDLNDRSFDLSAGGENSISVPSSTSTMKTGPLIS--SSQGRNSPA
ParentalPAVTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTHLQEMQQLQEM
.AV..ASVTNI.ATE.S..QVN.SESSG....ESIP....QPAI.P.PKP.V.RVVSST.L.....LQE.
RetrocopyLAVMTASVTNIRATEISLQQVNTSESSGAALNESIPHAVSQPAIAPSPKPMVTRVVSSTCLISHPDLQET
ParentalQQQKYLLL
QQQ.Y..L
RetrocopyQQQTYRIL

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 .24 RPM 99 .18 RPM
SRP051959_heart 1 .14 RPM 79 .07 RPM
SRP051959_kidney 0 .13 RPM 99 .35 RPM
SRP051959_liver 0 .02 RPM 87 .49 RPM
SRP051959_lung 0 .89 RPM 113 .47 RPM
SRP051959_lymph_node 0 .21 RPM 137 .71 RPM
SRP051959_skeletal_muscle 0 .31 RPM 58 .79 RPM
SRP051959_spleen 0 .08 RPM 114 .77 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_1763 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1763 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1763 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_30
Pan troglodytes retro_ptro_2595
Gorilla gorilla retro_ggor_202
Pongo abelii retro_pabe_3113
Macaca mulatta retro_mmul_1675
Mus musculus retro_mmus_37
Rattus norvegicus retro_rnor_863
Bos taurus retro_btau_1078
Canis familiaris retro_cfam_1783
Parental genes homology:
Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000141421 retrocopy
retro_amel_517,
Bos taurus ENSBTAG000000040541 retrocopy
retro_btau_1078,
Canis familiaris ENSCAFG000000177831 retrocopy
retro_cfam_1783,
Callithrix jacchus ENSCJAG00000006512 2 retrocopies
retro_cjac_1763 , retro_cjac_543,
Homo sapiens ENSG000000900601 retrocopy
retro_hsap_30,
Gorilla gorilla ENSGGOG000000062871 retrocopy
retro_ggor_202,
Myotis lucifugus ENSMLUG000000109221 retrocopy
retro_mluc_1396,
Macaca mulatta ENSMMUG000000186101 retrocopy
retro_mmul_1675,
Monodelphis domestica ENSMODG000000128872 retrocopies
retro_mdom_1714, retro_mdom_1916,
Mustela putorius furoENSMPUG000000030541 retrocopy
retro_mputfur_1375,
Mus musculus ENSMUSG000000211111 retrocopy
retro_mmus_37,
Nomascus leucogenys ENSNLEG000000006251 retrocopy
retro_nleu_2771,
Otolemur garnettii ENSOGAG000000046111 retrocopy
retro_ogar_987,
Pongo abelii ENSPPYG000000061281 retrocopy
retro_pabe_3113,
Pan troglodytes ENSPTRG000000067041 retrocopy
retro_ptro_2595,
Pteropus vampyrus ENSPVAG000000139251 retrocopy
retro_pvam_360,
Vicugna pacos ENSVPAG000000064641 retrocopy
retro_vpac_378,


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