RetrogeneDB ID:

retro_cjac_3955

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL286409.1:503148..504900(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PML
Ensembl ID:ENSCJAG00000017890
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3955
ATGCAGCAGGAGCCTGCACCCGAACGACCTCCGGTGCCCCAGCAGGACCCCACCCGGCCCCACGCGCCCACCATGCCTCC
CCCCGACACCCCCTCTGAAGGCCGCCAGCCCAGCCCCAGCCACAGCCCTGCAGAACAAGCCACGGAGGAGTTCCAGTTTC
TGCGCTGCCAGAAATGCCAGGCCAAAGCCAAGTGCCCGAAGCTGCTGCCTTACCTGCACACGCTGTGCTCGGGATGCCTG
GAGGCGTCGGGCATGCAATGCCCTATCTGCCAGGCGCCCTGGACGCCAGGTGCAGACACACCTGCACTGGATAACGTCTT
TTTCGAGAGTCTGCAGCGGCGCCTGTCGGTGTACCGGCAGATCGTGGATGCACAGGCTGTGTGCACCCGCTGCAAAGAGT
CAGCCGACTTCTTGTGCTTTGAGTGCGAGCAGCTCCTCTGCGCCAAGTGCTTCGAGGCACACCAATGTTTCCTCAAGCAC
GAGGCCTGGCCCCTGGCAGAGCTGCGCAACCAGTCGGTGCGTGAGTTCCTGGACGGCACCCGCAAGACCAACAACATCTT
CTGCTCTAACCCCAACCACCGCACCCCTATGCTGACCAGCATCTACTGCCGCGACTGTTCCAAGCCGCTGTGCTGCTCGT
GCGTGCTCTTTGACAGCGGCCACACCGAGCTAAAGTGCGACATCAGCGCGGAGATCCAGCAGCGACCGGAGGAGCTGGAT
GCCATGACGCAGGCGCTGCAGGAGCAGGACTGCGCCTTCGGTGGGGCGCACGCGCAGATGCACGCGGCCGTCGGCCAGCT
GGGCCGCGTGCGGGCGGAAACCGAGGAGCTGATCCGCGCGGGCATGCGCCAGGTAGTAGCTCACGGGCAGGCGCAGGAGA
CCGAGCTGCTGGAGGCGGTGGAGGCGCGGTAGCAGCGCGACTACGAGGAGATGGCCAGCCGGCTGGGCCGCCTGGACGCT
GTGCTACAGCGCATCCGCACGGGCAGCGCGCTCGTGCAGAGGATGAAGTGCTATGCCTCGGACTAGGAGGTGCTGGAGAT
GCACGGTTTCCTGCGCCAGGCACTCTGCCGTCTGCGCTAGGAGGAGCCCCAGAGCCAGCAAGCTGCCTTGCGCACGGATG
GCTTCGACGAGTTCAAGGTGCGCCTGCAGGACCTCATCTCTTACATCACCCAGGGGACAGATGCAGCTGTATCCAAGAAA
GCCAGGCCAGAGGCTGCCAGCACTCCCAGGGACCCTATTGATGTTGACCTGCCCGAGGAGGCAGAGAGAGTGAAGGCCCA
GGACCAGGCCCTGGGGCTGGCTGAAGCCCAACCTGTGGCTGTGGTACAGTCATTCCCCGGGGCACACCTCGTGCCAGTGT
ACGCCTTCTCCATCAAAGGCCCTTCCTACAGAGAGGAGGTCTCCAATACAACCACAGGCCAGAAAAGGAAGATCATTCAG
ACCCAGCGCCTCAGGAAGGTCATCCAGGAGTCTGAGGAGGGTAAGGAGGCGAGGTTGGCTCGGAGCTCCCCCGAGCAGCC
CAGGCGTAGCACCTCTAAGGCAGTCTCACCACCCCACTTGGATGGGCCGCCCAGCGCCGGGACCCCCGACATGGGAAGTG
AGGCCATCCCACCCAACAGCAACCATGTGGCCAGTGGCGCCGGGGAGGCAGAGGAGTGCATTGTGGTGATCAGCAGCTCA
GAAGACTCAGATGCCGAAAACTCGTGCATGGAGCCCACGGAGACCGCCAAGCCACAGTCCTCGCCAGCCCAG

ORF - retro_cjac_3955 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.4 %
Parental protein coverage: 66.4 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQQEPAPARSPGPQQDTARPHAPTMPPPDTPSEGRQPSPSHSPAEQATEEFQFLRCQKCQAEAKCPKLLP
MQQEPAP.R.P.PQQD..RPHAPTMPPPDTPSEGRQPSPSHSPAEQATEEFQFLRCQKCQA.AKCPKLLP
RetrocopyMQQEPAPERPPVPQQDPTRPHAPTMPPPDTPSEGRQPSPSHSPAEQATEEFQFLRCQKCQAKAKCPKLLP
ParentalCLHTLCSGCLEASGMQCPICQAPWPPGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADFWCF
.LHTLCSGCLEASGMQCPICQAPW.PGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADF.CF
RetrocopyYLHTLCSGCLEASGMQCPICQAPWTPGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADFLCF
ParentalECEQLLCAKCFEAHQWFLKHEARPLAELRNQSVREFLDGTRKTNNIFCSNPNHRTPTLTSIYCRGCSKPL
ECEQLLCAKCFEAHQ.FLKHEA.PLAELRNQSVREFLDGTRKTNNIFCSNPNHRTP.LTSIYCR.CSKPL
RetrocopyECEQLLCAKCFEAHQCFLKHEAWPLAELRNQSVREFLDGTRKTNNIFCSNPNHRTPMLTSIYCRDCSKPL
ParentalCCSCALLDSGHSELKCDISAEIQQRQEELDAMTQALQEQDGAFGAAHAQMHAAVGQLGRARADTEELIRA
CCSC.L.DSGH.ELKCDISAEIQQR.EELDAMTQALQEQD.AFG.AHAQMHAAVGQLGR.RA.TEELIRA
RetrocopyCCSCVLFDSGHTELKCDISAEIQQRPEELDAMTQALQEQDCAFGGAHAQMHAAVGQLGRVRAETEELIRA
ParentalRVRQVVAHVQAQESELLEAVEARYQRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASDQEVLDMHGF
..RQVVAH.QAQE.ELLEAVEAR.QRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASD.EVL.MHGF
RetrocopyGMRQVVAHGQAQETELLEAVEAR*QRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASD*EVLEMHGF
ParentalLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLISCITQGTDAAVSKQARPEAASTPRDPIDVDLPEE
LRQALCRLR.EEPQS.QAA.RTDGFDEFKVRLQDLIS.ITQGTDAAVSK.ARPEAASTPRDPIDVDLPEE
RetrocopyLRQALCRLR*EEPQSQQAALRTDGFDEFKVRLQDLISYITQGTDAAVSKKARPEAASTPRDPIDVDLPEE
ParentalAERVKAQAQALGLAEAQPVAVVQSVPGAHPVPVYAFSIKGPSYREEVSNTTTGQKRKSIQTQCPRKVIKM
AERVKAQ.QALGLAEAQPVAVVQS.PGAH.VPVYAFSIKGPSYREEVSNTTTGQKRK.IQTQ..RKVI..
RetrocopyAERVKAQDQALGLAEAQPVAVVQSFPGAHLVPVYAFSIKGPSYREEVSNTTTGQKRKIIQTQRLRKVIQ-
ParentalESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGLPSAESPDIGSEVILPNSNHVASGAGEAEERIVVISS
ESEEGKEARLARSSPEQPR.STSKAVSPPHLDG.PSA..PD.GSE.I.PNSNHVASGAGEAEE.IVVISS
RetrocopyESEEGKEARLARSSPEQPRRSTSKAVSPPHLDGPPSAGTPDMGSEAIPPNSNHVASGAGEAEECIVVISS
ParentalSEDSDAENSSSRELDDSSSESSDLQ
SEDSDAENS...........SS..Q
RetrocopySEDSDAENSCMEPTETAKPQSSPAQ

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 .00 RPM 7 .41 RPM
SRP051959_heart 0 .07 RPM 4 .60 RPM
SRP051959_kidney 0 .00 RPM 6 .08 RPM
SRP051959_liver 0 .02 RPM 3 .77 RPM
SRP051959_lung 0 .07 RPM 8 .83 RPM
SRP051959_lymph_node 0 .07 RPM 8 .77 RPM
SRP051959_skeletal_muscle 0 .00 RPM 1 .27 RPM
SRP051959_spleen 0 .00 RPM 11 .45 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_3955 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3955 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3955 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 ENSCJAG00000017890 1 retrocopy
retro_cjac_3955 ,


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