RetrogeneDB ID:

retro_cjac_3923

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL286262.1:31092..33497(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TRIM24
Ensembl ID:ENSCJAG00000012885
Aliases:None
Description:tripartite motif containing 24 [Source:HGNC Symbol;Acc:11812]


Retrocopy-Parental alignment summary:






>retro_cjac_3923
GAGATTCAGTTATTAGAACATAAAGAGCATAGATATCAATTTATAGAAGAAGCTTTTCAGAATCAGAAAGTGATCATAGA
TACACTAATCACCAAACTGATGGAAAAAACAAAATACATAAAATTCGCAGGAAATCAGATCCAAAACAGAATTAGTGAAG
TCAATCAAAATCAAAAGCAGGTGGAACAGGATATTAAAGTTGCTATATTTACATTGGTGGTAGAAATACATAAAAAAGGA
AAAGCTCTACTGCATCAGTTAGAGAGCCTTGCAAAAGACCATCGCATGAAACTATGCAACAACAACAGGAAGTGGCTGGA
CTTTCTAAACAATTGGAGCATGCCATGCATTTTTCTAAATGGGCAGTTTCCAGTGGCAGTAGTACAGCATTACTTTATAG
CAAAGGACTGATTACATACCGGTTGCGGCACCTCCTCCGTGCAAGATGTGATGCGTCCCCAGTGACCAACAACACCATCC
AGTTTCACTGTGATCCTAGTTTCTGGGCTCAAAATATTATCAACTTAGGTTCTTTAGTAATCGAGGATAAAGAGAGCCAG
CCACAAATGCCTAAGCAGAATCCTGTCGTGGAACAGAATTCACAGCCACCAAGTGGTTTATCATCAAACGAGTTATCCAA
GTTCCCAACACAGATCAGCCTAGCTCAATTACGGCTCCAGCATATGCAGCAACAGGTAATGGCTCAGGGGCAACAGGTGC
AGCGGAGGCCAGCACCTGTGGGTTTACCAAACCCTAGAATGCAGGGGCCCATCCAGCAACCTTCCATCTCTCATCAGCAA
CCCCCTCCACGTTTGATAAACTTTCAGAATCATAGCCCCAAACCCAATGGACCAGTTCTTCCTCCTCATTCTCAACAACT
GAGATATCCACCAAACCAGAATATACCATAACAAGCAATAAAGCCCAACCCCCTACAAATGGCTTTCTTGGCTCAAGCCA
TAAAACAGTGGCAGATCAGCAGGGGACAGGGTGACCATCAACTACCAACAGCGCATCCTCTACTCCTTCCAGCCCCGCGA
TTGCTAGTGCAGCAGGATGTAATGGAAAGGCTTTTGGTTCACCTATGATCGATTTAAGCCCACCAGTGGGAGCTTCATAT
AATCTTCCCTCTCTTCCAGATATTGACTGTTCAAATACTATTATGCTGGACAATATTGTGAGGAAAGATACTAATATAGA
TCATGGCCAGCCAAGACCACGCTCAAACAGAACGGTCCAGTCACCAAATTTATCAGTGCCATCTCCAGGCCTAGCAGGAC
CTGGTATTATGACTAATGTACACCCCTCAATAAGTTCACTTAGTGCCTCCAGCGTTGGAAGCCGAGGAAGCCCTGGCCCT
TCCAGCAAACCAGCAGAAGCTGATTCTACACACAAAGTCCCAGTGGTGACGTTGGAGCCAATTCGAATAAAACAAGAAAA
CAGTGGACCAACTGAAAATTATGATTTCCCTGTTGTTATAGTGAAGCAAGAATCAGATGAAGAATCCAGGCCTCAAAATG
CCAATTATCCAAGAAGCGTACTCACCTCCCTGCTCTTAAATAGCAGCCAGAGCTCTACTTCTGAGGAGACAGTGCTAAGA
TCAGACGCCCCTGATAGTACAGATCAACCTGGACTTCACCAGGAGAATTCCTCGAATGGAAAGTCTGAGTGGCTGGATCC
TTCCCAGAAGTCACCCCTTCACATTGGAGAGACAAGGAAAGAGGATGATCCAAATGAGGACTGGTGTGCAGGTTGCCAAA
ATGGAGGGGAACTCCTGTGCTGTGAAAAGTGCCCCAAAGTATTCCATCTTTCTTGTCATGTGCCCACATTGACAAATTTT
CCAAGTGGAGAGTGGATTTGCACTTTCTGCTGAGACTTTTCTAAACCAGAAGTTGACTATGATTGATGCTCCCAGGCACA
ACTCAGAACAAAGGAAAACTGAAGGCCTTGTTAAATTATCACCTATAGATAAAAGGAAGTGTGAGCGCCTACTTTTATTT
CTTCACTGCCATGAAAGGAGCCTGGCTTTTCAAGACCCTGTTCCTCTAACTGTGCCCGATTATTCCAAAATAATTAAAAA
TCCGATGGATTTGCCAACCATCAAGAAGAGACTACAAGAAGATTATTCCATGTACTCAAAACCTGAAGATTTTGTAGCTG
ATTTTAGATTGAGCTTTCAAAACTGTGCTCAATTCAATGAGCCTGATTCAGAAGTAGCTAATGCTGGTATAAAACTTGAA
AATTATTTTGAAGAACTTCTAAAGAACCTCTATCCAGAAAAGAGATTTCCTAAACCAGAATTCAGGAATGAATCCGAAGT
TAATAAATACAGTGATGATTCAGATGATGACTTTGTACAGCCCTGAAAGAAACGCCTCAAAAGCACTGAAGAATGACAGT
TGCTT

ORF - retro_cjac_3923 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.1 %
Parental protein coverage: 77.18 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalDCQLLEHKEHRYQFIEEAFQNQKVIIDTLITKLMEKTKYIKFTGNQIQNRIIEVNQNQKQVEQDIKVAIF
..QLLEHKEHRYQFIEEAFQNQKVIIDTLITKLMEKTKYIKF.GNQIQNRI.EVNQNQKQVEQDIKVAIF
RetrocopyEIQLLEHKEHRYQFIEEAFQNQKVIIDTLITKLMEKTKYIKFAGNQIQNRISEVNQNQKQVEQDIKVAIF
ParentalTLMVEINKKGKALLHQLESLAKDHRMKL-MQQQQEVAGLSKQLEHVMHFSKWAVSSGSSTALLYSKRLIT
TL.VEI.KKGKALLHQLESLAKDHRMKL.MQQQQEVAGLSKQLEH.MHFSKWAVSSGSSTALLYSK.LIT
RetrocopyTLVVEIHKKGKALLHQLESLAKDHRMKL<MQQQQEVAGLSKQLEHAMHFSKWAVSSGSSTALLYSKGLIT
ParentalYRLRHLLRARCDASPVTNNTIQFHCDPSFWAQNIINLGSLVIEDKESQPQMPKQNPVVEQNSQPPSGLSS
YRLRHLLRARCDASPVTNNTIQFHCDPSFWAQNIINLGSLVIEDKESQPQMPKQNPVVEQNSQPPSGLSS
RetrocopyYRLRHLLRARCDASPVTNNTIQFHCDPSFWAQNIINLGSLVIEDKESQPQMPKQNPVVEQNSQPPSGLSS
ParentalNQLSKFPTQISLAQLRLQHMQQQVMAQRQQVQRRPAPVGLPNPRMQGPIQQPSISHQQPPPRLINFQNHS
N.LSKFPTQISLAQLRLQHMQQQVMAQ.QQVQRRPAPVGLPNPRMQGPIQQPSISHQQPPPRLINFQNHS
RetrocopyNELSKFPTQISLAQLRLQHMQQQVMAQGQQVQRRPAPVGLPNPRMQGPIQQPSISHQQPPPRLINFQNHS
ParentalPKPNGPVLPPHPQQLRYPPNQNIPRQAIKPNPLQMAFLAQQAIKQWQISSGQGA-PSTTNSTSSTPSSPT
PKPNGPVLPPH.QQLRYPPNQNIP.QAIKPNPLQMAFLA.QAIKQWQIS.GQG..PSTTNS.SSTPSSP.
RetrocopyPKPNGPVLPPHSQQLRYPPNQNIP*QAIKPNPLQMAFLA-QAIKQWQISRGQGD<PSTTNSASSTPSSPA
ParentalITSAAGYDGKAFGSPMIDLSSPVGGSYNLPSLPDIDCSSTIMLDSIVRKDTNIDHGQPRPPSNRTVQSPN
I.SAAG..GKAFGSPMIDLS.PVG.SYNLPSLPDIDCS.TIMLD.IVRKDTNIDHGQPRP.SNRTVQSPN
RetrocopyIASAAGCNGKAFGSPMIDLSPPVGASYNLPSLPDIDCSNTIMLDNIVRKDTNIDHGQPRPRSNRTVQSPN
ParentalSSVPSPGLAGPVTMTSVHPPIRSPSASSVGSRGSSGSSSKPAGADSTHKVPVVMLEPIRIKQENSGPPEN
.SVPSPGLAGP..MT.VHP.I.S.SASSVGSRGS.G.SSKPA.ADSTHKVPVV.LEPIRIKQENSGP.EN
RetrocopyLSVPSPGLAGPGIMTNVHPSISSLSASSVGSRGSPGPSSKPAEADSTHKVPVVTLEPIRIKQENSGPTEN
ParentalYDFPVVIVKQESDEESRPQNANYPRSILTSLLLNSSQSSTSEETVLRSDAPDSTGDQPGLQQENSSNGKS
YDFPVVIVKQESDEESRPQNANYPRS.LTSLLLNSSQSSTSEETVLRSDAPDST.DQPGL.QENSSNGKS
RetrocopyYDFPVVIVKQESDEESRPQNANYPRSVLTSLLLNSSQSSTSEETVLRSDAPDST-DQPGLHQENSSNGKS
ParentalEWLDPSQKSPLHVGETRKEDDPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRD
EWLDPSQKSPLH.GETRKEDDPNEDWCA.CQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFC.D
RetrocopyEWLDPSQKSPLHIGETRKEDDPNEDWCAGCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFC*D
ParentalLSKPEVEYD-CDAPSHNSEKRKTEGL-VKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIK
.SKPEV.YD....P.....K.K...L.VKL.PIDKRKCERLLLFL.CHE.SLAFQDPVPLTVPDY.KIIK
RetrocopyFSKPEVDYD<LMLPGTTQNKGKLKAL<VKLSPIDKRKCERLLLFLHCHERSLAFQDPVPLTVPDYSKIIK
ParentalNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPEKRF
NPMDL.TIKKRLQEDYSMYSKPEDFVADFRL.FQNCA.FNEPDSEVANAGIKLENYFEELLKNLYPEKRF
RetrocopyNPMDLPTIKKRLQEDYSMYSKPEDFVADFRLSFQNCAQFNEPDSEVANAGIKLENYFEELLKNLYPEKRF
ParentalPKPEFRNESEDNKYSDDSDDDFVQPRKKRLKSIEERQLL
PKPEFRNESE.NKYSDDSDDDFVQP.KKRLKS.EE.QLL
RetrocopyPKPEFRNESEVNKYSDDSDDDFVQP*KKRLKSTEE*QLL

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 .09 RPM 22 .76 RPM
SRP051959_heart 0 .14 RPM 14 .40 RPM
SRP051959_kidney 0 .09 RPM 23 .05 RPM
SRP051959_liver 0 .13 RPM 14 .95 RPM
SRP051959_lung 0 .36 RPM 16 .32 RPM
SRP051959_lymph_node 0 .21 RPM 12 .85 RPM
SRP051959_skeletal_muscle 0 .46 RPM 6 .75 RPM
SRP051959_spleen 0 .19 RPM 11 .76 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_3923 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3923 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3923 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000012885 1 retrocopy
retro_cjac_3923 ,
Dasypus novemcinctus ENSDNOG000000065331 retrocopy
retro_dnov_1442,


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