RetrogeneDB ID:

retro_cjac_3909

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL286228.1:4276..6260(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBAP2L
Ensembl ID:ENSCJAG00000009677
Aliases:None
Description:ubiquitin associated protein 2-like [Source:HGNC Symbol;Acc:29877]


Retrocopy-Parental alignment summary:






>retro_cjac_3909
GCATGGAGGACTGCAACAGAGGAATGGGGGACTGAAGATTGGAATGAAGATCTTTCTGAGACCAAGATCTTCACTGCCTC
TAATGTGTCTTCAGTGCCTCTGCCTGTGGAGAATGTGACAATCACTGCTGGTCAGAGAATTGACCTTGCTGTTCTTCTCG
GGAAGACACCATCTACAATGGAGAATGATTCATCTAATCTGGATCCATCTCAGGCTCCTTCTCTGGCCCAGCCTCTGGTG
TTCAGCAACTCAAAGCAGACTCCACAACACAGCCGGCTTCAGGGAACACATTTTCTCATCACAGTATGGTGAGCCTGCTG
GGGAAAGGATTTGGTGATGGTGAATGAAGCTAAAGGCGGCAGTACTACGGGCTCCCAGTTCTTGGAGCAATTCAAGACTG
CTCAAGCCCTGGCTCAGTTGGCAGTTCAGCATTCTTAGACTGGAAGCACCACCACCTCCTCTTGGGACATGGGCTTGATG
ACACAATCCCCATCATTGGTGTAGTATGATTTGAAGAACCCAAATGATTCAACAGTGCACAGCCCCTTTATAAAGCGCCA
GGCTTTTACCCCATCTTCAACCATGATGGAGGTGTTCCTTCAGGAGAAGTCACCTGCAGTGGCTACCTCCACAGCTGCAC
CTCCACCTCAGTCTTCTCCTCTGCCAAGGAAATCCACATCGGCTCCATCGATGTCACCTAGATCTTCAGACAACCAGTCC
TCTAGCCCTAGCCAGCTCAGAAAAAGCTGAAACAGCAGGAGAAAAAAGCCTCCTTGACTTCTAAGATTCCTGCTCTGGCT
GTGGAGATGCCTGGCTCAGCAGCTATCTCAGGGCTAAACCTGCAGTTTGGGGCATTGCAGTTTGGGTCAGAGCCAGTCCT
TTCTGATTATGAGTCCACCCCTACCACGAGCGCCTCTTCAAGCCAGCTCCAGTAGCCTATATACCAGCACGGCCAGCGAA
TCTTCATCTACAATTTGATCTAACCAGAGTCAGGAGTCGTTATCAGAGTGGCCCAATTCAGTCGACAACCTATACCTCCC
AAAATAATGCTCAGGGCCCTCTTTATGAACAGAGATCCACACAGACTCGGTGGTACCCCAGCTCCATCTTTTCATCACCC
CAAAAGGACCTGACTCAGGCAAAGAATGGCTTCAGTTCTGTGCAGGCCACACAATTACGGACCACTCAATCTGTTGAAGG
TGCTACAAGCTCTGCAGTAAAATCTGATTTACCCTCCACTTCTAGCATCCCCGCTCTCAATGAAATGGTATCTGCACCTT
CCTTAGTGACAACAACCAATCTGCACTCATCCTCCTTGGGTGGCTTGAGCCACAGTGAGGAGATTCGAAATACTAACACC
ACACAACACAGCAGCACATTATCTACGCAGCAGAATACCCTTTCGTCATCAACATCTTCTGGGCACACTTCAACATCCAC
TCTTTTGCACACAAGCATGGAGAGTGAAACGAATCTCTATTCTTCCTCCAGCACTTTTTCCACCACATCCAGCACAGTCT
CTGCACCTCCCCCAGTGGTCAGTGTCTCCTCCACTCTCAATAGTGGCAGTAGTCTGGGTCTCAGCCTAGGCTGCAACTCC
CCTGTCACAGCCTCGACTCGAAGTTCAGTTGCCACGACTTCAGGAAAAGCTCCTCCCAGCCTCCCTCCTGGGGTCCCACC
GTTGTTGCCTAATCCGTGTATTGTGGCTCCAGGGCTGTTACATGCCTATCCGCCACAAGTATATGGTTATGATGACTTGC
AGATGCTTCAAACAAGATTTCCATTGTATTACTACAGCATCCTATTTCCCACACTCACTACTCCGCTGACTGGGGGGGAT
GGTAGCCTGGCCGGCAACCCTTATTCTGGTGACCTCACAAAGTTCGGCCTTTGGGATGCCTCCTCCCCAGCCCCGGCCAC
AACCTTGGCCCAACCCCAACAGAACCAGACGCAGAATCACCACACCACGCAGCAGACATTCCTG

ORF - retro_cjac_3909 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.53 %
Parental protein coverage: 61.17 %
Number of stop codons detected: 3
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalAWRTATEEWGTEDWNEDLSETKIFTASNVSSVPLPAENVTITAGQRIDLAVLLGKTPSTMENDSSNLDPS
AWRTATEEWGTEDWNEDLSETKIFTASNVSSVPLP.ENVTITAGQRIDLAVLLGKTPSTMENDSSNLDPS
RetrocopyAWRTATEEWGTEDWNEDLSETKIFTASNVSSVPLPVENVTITAGQRIDLAVLLGKTPSTMENDSSNLDPS
ParentalQAPSLAQPLVFSNSKQT-AISQPASGNTFSHHSMVSMLGKGFGD-VGEAKGGSTTGSQFLEQFKTAQALA
QAPSLAQPLVFSNSKQT....QPASGNTFSHHSMVS.LGKGFGD.V.EAKGGSTTGSQFLEQFKTAQALA
RetrocopyQAPSLAQPLVFSNSKQT<STTQPASGNTFSHHSMVSLLGKGFGD>VNEAKGGSTTGSQFLEQFKTAQALA
ParentalQLAAQHSQSGSTTTSSWDMGSTTQSPSLVQYDLKNPNDSTVHSPFTKRQAFTPSSTMMEVFLQEKSPAVA
QLA.QHS..GSTTTSSWDMG..TQSPSLV.YDLKNPNDSTVHSPF.KRQAFTPSSTMMEVFLQEKSPAVA
RetrocopyQLAVQHS*TGSTTTSSWDMGLMTQSPSLV*YDLKNPNDSTVHSPFIKRQAFTPSSTMMEVFLQEKSPAVA
ParentalTSTAAPPPPSSPLPSKSTSAPQMSPGSSDNQSSSPQ-PAQQKLKQQKKKASLTSKIPALAVEMPGSADIS
TSTAAPPP.SSPLP.KSTSAP.MSP.SSDNQSSSP..PAQ.KLKQQ.KKASLTSKIPALAVEMPGSA.IS
RetrocopyTSTAAPPPQSSPLPRKSTSAPSMSPRSSDNQSSSPS<PAQKKLKQQEKKASLTSKIPALAVEMPGSAAIS
ParentalGLNLQFGALQFGSEPVLSDYESTPTTSASSSQ-AP-SSLYTSTASESSSTISSNQSQE-SGYQSGPIQST
GLNLQFGALQFGSEPVLSDYESTPTTSASSSQ.AP.SSLY.......SS..........S.YQSGPIQST
RetrocopyGLNLQFGALQFGSEPVLSDYESTPTTSASSSQ<AP<SSLY-TSTASESSSTI*SNQSQ>SRYQSGPIQST
ParentalTYTSQNNAQGPLYEQRSTQTRRYPNSISSSPQKDLTQAKANGAKKLEVVIGKLKKAHIFLGATGSAVKSD
TYTSQNNAQGPLYEQRSTQTR.YP.SI.SSPQKDLTQAK.NG..........L.......GAT.SAVKSD
RetrocopyTYTSQNNAQGPLYEQRSTQTRWYPSSIFSSPQKDLTQAK-NGFSSVQAT--QLRTTQSVEGATSSAVKSD
ParentalSPSTSSIPPLNETVSAASLLTTTNQHSSSLGGLSHSEEIPNTTATQHSSSVQATQLQTTQSVEVSESRCQ
.PSTSSIP.LNE.VSA.SL.TTTN.HSSSLGGLSHSEEI.NT..TQHSS....TQ.Q.T.S...S.....
RetrocopyLPSTSSIPALNEMVSAPSLVTTTNLHSSSLGGLSHSEEIRNTNTTQHSSTL-STQ-QNTLSSSTSSGHTS
ParentalLSPLKHTSVESEANLHSSSSTFSTTSSTVSAPPPVVSVSSSLNSGSSLGLSLGSNSTVTASTRSSVATTS
.S.L.HTS.ESE.NL.SSSSTFSTTSSTVSAPPPVVSVSS.LNSGSSLGLSLG.NS.VTASTRSSVATTS
RetrocopyTSTLLHTSMESETNLYSSSSTFSTTSSTVSAPPPVVSVSSTLNSGSSLGLSLGCNSPVTASTRSSVATTS
ParentalGKAPPNLPPGVPPLLPNPYIMAPGLLHAYPPQVYGYDDLQMLQTRFPLDYYSIPFPTPTTPLTGREGSLA
GKAPP.LPPGVPPLLPNP.I.APGLLHAYPPQVYGYDDLQMLQTRFPL.YYSI.FPT.TTPLTG..GSLA
RetrocopyGKAPPSLPPGVPPLLPNPCIVAPGLLHAYPPQVYGYDDLQMLQTRFPLYYYSILFPTLTTPLTGGDGSLA
ParentalSNPYSGDLTKFGRGDASSPAPATTLAQPQQNQTQTHHTTQQTFL
.NPYSGDLTKFG..DASSPAPATTLAQPQQNQTQ.HHTTQQTFL
RetrocopyGNPYSGDLTKFGLWDASSPAPATTLAQPQQNQTQNHHTTQQTFL

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 .33 RPM 27 .49 RPM
SRP051959_heart 0 .28 RPM 30 .94 RPM
SRP051959_kidney 0 .31 RPM 37 .69 RPM
SRP051959_liver 0 .19 RPM 21 .77 RPM
SRP051959_lung 0 .55 RPM 38 .31 RPM
SRP051959_lymph_node 0 .34 RPM 37 .58 RPM
SRP051959_skeletal_muscle 0 .50 RPM 28 .96 RPM
SRP051959_spleen 0 .29 RPM 39 .08 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_3909 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3909 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3909 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 ENSCJAG00000009677 1 retrocopy
retro_cjac_3909 ,


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