RetrogeneDB ID:

retro_cjac_517

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:37577466..37579985(-)
Located in intron of:ENSCJAG00000021196
Retrocopy
information
Ensembl ID:ENSCJAG00000035406
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KDM1A
Ensembl ID:ENSCJAG00000005607
Aliases:None
Description:lysine (K)-specific demethylase 1A [Source:HGNC Symbol;Acc:29079]


Retrocopy-Parental alignment summary:






>retro_cjac_517
TCGGCGGCCCGGCGGCCCGAGATGTTGTCTGGGAAGAAGGCGGTAGCCGGGACAGACAGTGCCGAGAACGGCTCTGAGGT
GGCCGCGCCGCCCGCAGGCCTGTCGGGCCCAGCCGAGGTCGGGCAGGGGGCGGCCGGGGAGCGCACGCCCCGCAAGAAAG
AGCCTCCGCGGGCCTCGCCCCCCCGGGGGCCTGGCCGAACCGCCGGGGTCCACAGGGCCTCAGGCCGGGCCTACCGTCGT
GCCTGGGTCTGCGACCCCCATGGAAACTGGAATAGCAGAGACTCCGGAGGGGCGTCGGCCTAGCAGGCGCAAGCGGGCGA
AGGTAGAGTACAGAGAGATGGGTGAAAGCTTGGCCAACCTCTCAGAAGATAAGTATTATTCAGAAGAAGAGAGAAATGCT
AAAGCAGAGAAGGAAAAGAAGCTTCCCCCACCACCTCCTCAAGCCCCACCTGAGGAAGAAAACGGAAGTGAGCCTGAAGA
ACCATCGGGGGTGGAGGGAGCAGCTTTCCAGAGCCGACTTCCTCATGACCGGATGACTTCTCAAGAAGCAGCCTGTTTTC
CAGATATTATCAGTGGACCACAGCGGACCCAGAAAGCTTTTCTGTTCATTAGAAACCACACGTTGCAGTTGCGGTTGGAT
AATCCAAAGATTCAACTGACATTTGAGGCTACTCTCCAACAATTAGAAGCACCTTATAACAGTGATACTGTGCTTCTCCA
CCGAGTGCACAGTTATTTGGAGCGGCATGGTCTTATCAACTGTGGCATCTATAAAAGGACAAAACCCCTACCAACTAAAA
AGACAGGAAAGGTCATTATTATAGCCCCTGGGGTCTCAGGCTTGGCAGCAGCTAGACAGTTACAAAGTTTTGGAATGGAT
GTCATACTTTTGGAAGCCAGGGATCGTGTGGGTGGACGAGTTGCTACGTTTCGCAAAGGAAACTATGTAGCTGATCTTGG
AGCCACGGTGATAACAGGTCTTGGAGGGAATCCTATGGCTGTTGTCAGCAAACAAGTAAATATGGAACTGGCCAAGATCA
AGCAAAAATGCCCACTTTATGAAGCAAACGGACAAGCTGTTCCTAAAGAGAAAGATGAAATGGTAGAGCAAGAGCTTAAC
CGGTTGCTAGAAGCTACATCTTACCTTAGTCATCAGCTAGACTTCAATGTCCTCACTAATAAACCTGTGTCTCTTGGCCA
GGTATTAGAAGTTGTCATTCAGTTGCAAGAAAAGCATGTCAAAGATGAGCAGATTGAACATTGGAAGAAGATAGTGAAAA
CTCAGGAAGAATTGAAAGAACTTCTTAATAAGACGGTAAATTTGAAAGAGAAAATCAAAGAACTCCATCAGCAATACAAA
GAAGCATCTGAAGTAAAGCCACCCAGAGACATTACTGCCGAGTTCTTAGTGAAAAGCAAACACAGGGATCTGACCGCCCT
ATGCAAGGAATATGATGAATTAGCTGAAACACAAGGAAAGCTAGAAGAAAAACTTCAGGAATTGGAAGCGAATCCTCCAA
GTGATGTATATCTCTCCTCAAGAGACAGACAAATACTTGACTGGCATTTTGCAAATCTTGAATTTGCTAATGCCACACCT
CTCTCAACTCTCTCCCTTAAACACTGGGATCAGGATGATGACTGAGTTCACTGGCATCCAACTGACGGTGAGGAATGGCT
ACTCATGTGTGCCTGTGGCTTTAGCAGAAGGCCTAGACATTAAACTGAATACAGCAGTGCGACAGGTTCACTACACGGCT
TCAGGATGTGAAGTGATAGCTGTGAATACCCGCTCCACAAGTCAAACCTTTATTTATAAATGCGATGCAGTTCTCTGTAC
CCTTCCCCTGGGTGTGCTGAAGCAGCAGCCACCAGCTGTTCAGTTTGTGCCACCTCTTCCTGAGTGGAAAACATCTGCAG
TCCAAAGGATGGGATTTGGCAGTCTTAATAAGGTGGTGTTGTGTTTTGACTGGGTGTTCTGGGATCCAAGTGTCAATTTG
TTTGGGCATGTTGGCAGTACGACTTCCAGCAGGGGTGAGCTATTCCTCTTCTGGAATCTCTATAAAGCTCCAATACTGTT
GGCACTAGTGGCAGGAGAAGCTGATGGTATCATGGAAAATATAAGTAATGATGTGATTGTTGGCCGATGCCTGGCCATTC
TTAAAGGGATTTTTGGAAGCAGTGCAGTACCCCAGCCCAAAGAAACTGTGGTGTCTTGTTGGCGTGCTGATCCTTGGGCC
TGGGGCTCTTATTCCTATGTTGCTGCAGGATCATCTGGAAATGATTTAATGGCTCAGCCAATCACTCCTGGCCCATCAAT
TCCAGGCGCCCCACAGCCAATTCCACAACTCTTCTTTGCGGGAGAACATACGATCTCTAACTACCCAGCCACAGTGCATG
GTGCTCTGCTGAGTGGGCTGTGAGAAACAGGAAGAATTGCAGACCAGTTTTTGGGGGCCACGTATACGCTGCCTCACCAG
GCCACACCAGGTGTTCCTGCACAGCAGTCCCCAAGCATG

ORF - retro_cjac_517 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.14 %
Parental protein coverage: 98.94 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAAAAAAAAAAGTEAGPGTAGSAENGSEVAAPPAGLSGPAEVGPGAAGERTPRKKEPPRASPP-GGLAEPP
.AA.......G..A..GT..SAENGSEVAAPPAGLSGPAEVG.GAAGERTPRKKEPPRASPP.GGLAEPP
RetrocopySAARRPEMLSGKKAVAGT-DSAENGSEVAAPPAGLSGPAEVGQGAAGERTPRKKEPPRASPP>GGLAEPP
ParentalGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEYREMDESLANLSEDEYYSEEERNAKAEKE
GS.GPQAGPTVVPGSATPMETGIAETPEGRR.SRRKRAKVEYREM.ESLANLSED.YYSEEERNAKAEKE
RetrocopyGSTGPQAGPTVVPGSATPMETGIAETPEGRRPSRRKRAKVEYREMGESLANLSEDKYYSEEERNAKAEKE
ParentalKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTL
KKLPPPPPQAPPEEEN.SEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQ.TQK.FLFIRN.TL
RetrocopyKKLPPPPPQAPPEEENGSEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQRTQKAFLFIRNHTL
ParentalQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGV
QL.LDNPKIQLTFEATLQQLEAPYNSDTVL.HRVHSYLERHGLIN.GIYKR.KPLPTKKTGKVIII..GV
RetrocopyQLRLDNPKIQLTFEATLQQLEAPYNSDTVLLHRVHSYLERHGLINCGIYKRTKPLPTKKTGKVIIIAPGV
ParentalSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQ
SGLAAARQLQSFGMDV.LLEARDRVGGRVATFRKGNYVADLGA.V.TGLGGNPMAVVSKQVNMELAKIKQ
RetrocopySGLAAARQLQSFGMDVILLEARDRVGGRVATFRKGNYVADLGATVITGLGGNPMAVVSKQVNMELAKIKQ
ParentalKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQI
KCPLYEANGQAVPKEKDEMVEQE.NRLLEATSYLSHQLDFNVL.NKPVSLGQ.LEVVIQLQEKHVKDEQI
RetrocopyKCPLYEANGQAVPKEKDEMVEQELNRLLEATSYLSHQLDFNVLTNKPVSLGQVLEVVIQLQEKHVKDEQI
ParentalEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELA
EHWKKIVKTQEELKELLNK.VNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELA
RetrocopyEHWKKIVKTQEELKELLNKTVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELA
ParentalETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDD-FEFTGSHLTV
ETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQ.DD..EFTG..LTV
RetrocopyETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQ-DD>TEFTGIQLTV
ParentalRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAV
RNGYSCVPVALAEGLDIKLNTAVRQV.YTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAV
RetrocopyRNGYSCVPVALAEGLDIKLNTAVRQVHYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAV
ParentalQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALV
QFVPPLPEWKTSAVQRMGFG.LNKVVLCFD.VFWDPSVNLFGHVGSTT.SRGELFLFWNLYKAPILLALV
RetrocopyQFVPPLPEWKTSAVQRMGFGSLNKVVLCFDWVFWDPSVNLFGHVGSTTSSRGELFLFWNLYKAPILLALV
ParentalAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMA
AGEA.GIMENIS.DVIVGRCLAILKGIFGSSAVPQPKETVVS.WRADPWA.GSYSYVAAGSSGN..DLMA
RetrocopyAGEADGIMENISNDVIVGRCLAILKGIFGSSAVPQPKETVVSCWRADPWAWGSYSYVAAGSSGN--DLMA
ParentalQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQ
QPITPGPSIPGAPQPIP.LFFAGEHTI.NYPATVHGALLSGL.E.GRIADQFLGA.YTLP.QATPGVPAQ
RetrocopyQPITPGPSIPGAPQPIPQLFFAGEHTISNYPATVHGALLSGL*ETGRIADQFLGATYTLPHQATPGVPAQ
ParentalQSPSM
QSPSM
RetrocopyQSPSM

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 1 .77 RPM 19 .84 RPM
SRP051959_heart 1 .40 RPM 23 .63 RPM
SRP051959_kidney 1 .20 RPM 29 .06 RPM
SRP051959_liver 0 .87 RPM 16 .27 RPM
SRP051959_lung 2 .72 RPM 24 .74 RPM
SRP051959_lymph_node 4 .93 RPM 20 .04 RPM
SRP051959_skeletal_muscle 0 .68 RPM 19 .68 RPM
SRP051959_spleen 3 .78 RPM 24 .92 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_517 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_517 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_517 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 ENSCJAG00000005607 1 retrocopy
retro_cjac_517 ,


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