RetrogeneDB ID:

retro_cjac_2256

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:109497136..109498590(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:XRCC5
Ensembl ID:ENSCJAG00000012291
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2256
TGGCCCTGCCGACTGACCATTGGCTCCAATTTGTCTATAGGAATTGCATCCTATAAATTGATTCTACGGGTGAGAGAGTT
TAAAAGACCTGGGCAGTTGTGGATGCAAAAACCCTAAAAAAAAAAAGAAGATATACAAAAAGAAACAGTTTATTGCTTAA
ATGATGATGATGAAACTGGAGTTTTAAAAGAGGATATTATTCAAGTGTTCCTCTATGGAAGTGATATAGCTCCTTTCTCT
AAAGTGGATGAGGAACAAATGAAATATAAATTGGAAGGCAAGTGCTTCTCTGTTTTGAGATTTTGTAAATCTTCTCAGGT
TTAGAGAAGATTCTTCAAGGGAAATCAAGTTCTAAAGGTCTTTGCAGCAAGAGACGATGAGGCAGCAGCAGTTGCACTTT
CCTCCCTGATTTATGCTTTGGATGAGTTAGATGTGGTGGCCATAGTTTGATATGCTTATGACAAAAGAACTAATCCTCAA
GTCGGCATGGCTTTTCCTCACATCAAGCATAATCATGAGTGTTTAGTGTATGTGCAGCCACCTTTCATGGAAGACTTGCT
GCAATATCTGTTTTCATCCTTGAAAAACAGTGAGAAATATGCTCCCACCGAGGCACAGTTGAATGCTGTTGATGCTTCTA
TTGACTCCATGAGCTTGGTAAAGAAAGATGGGAAGACAGATACTCTTGAAGACTTGTTTCCAACCACCCAAATCTCAAAT
CCTCTATTTCACAGATTATTTCGGTGTCTGCTGCACAAAGCTTTACATCCCCAGGAGCCTCTACCCCCAACTCAGCAGCA
TATTTAGAATATGCTGAATCCTCCCACTGAGGTGACAGCAAAATGTCAAATTTCTCTCTCTAAAATAAAGACCCTTTTCC
CTCTGATGGAAGCCAAGAAAAAGGATCAAGTAACCATTCAGGACATTTTCCAAGACAACCATACAAATGGACCCATCTCT
AAAAAATTAATGACTGAGGAAGAGGGAGCCCACTTCAGCGTCTCCAGCCTGGCTGAAGACAGTGTCACCTCTGCTGGAAG
TGTGAATCCTACTGAAAACTTTCGTGTTCTAGTGAAACAGAAAAATGCCAGCTTTGAGGAAGCGAGTGTTCAGCTCATAA
ATCACATCAAACAGTTTTTGGATAATAATGGAACACAATATTTTACGAAGAGCAGGGACTGCATCAGAGCCTTCCAGAAA
GAAGCCATTAAGTTTCAAAAGAGCAGTGCTTTAACAACTTCCTGTAAGCGCTTTGAGAGAAAGTGGAAATTAAACAATTA
AATCATTTATGGGAAATTGTTGTTCAGGATGGAATTACTCTGATCACCAAAGAGGAAGCCTCTGGAAGATCTGTCACAGC
TGAGGAAGCCAAAAAGTTTCTGGCCGCCAAAGTAAAACCAAGTGAAGACACAGCAGCCGTATTTGAAGAAGGTGCTTATG
GGAACGATTTACTG

ORF - retro_cjac_2256 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.45 %
Parental protein coverage: 65.98 %
Number of stop codons detected: 6
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalWPCRLTIGSNLSIRIAAYKSILQER-VKKTWTVVDAKTLKK-EDIQKETVYCLNDDDETEILKEDIIQGF
WPCRLTIGSNLSI.IA.YK.IL..R..K........K..KK.EDIQKETVYCLNDDDET..LKEDIIQ.F
RetrocopyWPCRLTIGSNLSIGIASYKLILRVREFKRPGQLWMQKP*KKKEDIQKETVYCLNDDDETGVLKEDIIQVF
ParentalRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHAL
.YGSDI.PFSKVDEEQMKYK.EGKCFSVL.FCKSSQV.RRFF.GNQVLKVFAARDDEAAAVALSSLI.AL
RetrocopyLYGSDIAPFSKVDEEQMKYKLEGKCFSVLRFCKSSQV*RRFFKGNQVLKVFAARDDEAAAVALSSLIYAL
ParentalNDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAV
..LD.VAIV.YAYDKR.NPQVG.AFPHIKHN.ECLVYVQ.PFMEDL.QY.FSSLKNS.KYAPTEAQLNAV
RetrocopyDELDVVAIV*YAYDKRTNPQVGMAFPHIKHNHECLVYVQPPFMEDLLQYLFSSLKNSEKYAPTEAQLNAV
ParentalDALIDSMSLAKKDEKTNTLEDMFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPTEVTK
DA.IDSMSL.KKD.KT.TLED.FPTT.I.NP.F.RLF.CLLH.ALHP.EPLPP.QQHI.NMLNPPTEVT.
RetrocopyDASIDSMSLVKKDGKTDTLEDLFPTTQISNPLFHRLFRCLLHKALHPQEPLPPTQQHI*NMLNPPTEVTA
ParentalKSQIPLSKIKTLFPLIEAKKKDQVIAQDVFQDNHEDGPTAKKLKTEEGGAHFSISSLAEGSVTSVGSVNP
K.QI.LSKIKTLFPL.EAKKKDQV..QD.FQDNH..GP..KKL.TEE.GAHFS.SSLAE.SVTS.GSVNP
RetrocopyKCQISLSKIKTLFPLMEAKKKDQVTIQDIFQDNHTNGPISKKLMTEEEGAHFSVSSLAEDSVTSAGSVNP
ParentalAENFRVLVKQKKASFEEASNQLINHIEQFLDTNETLYFMKSMDCIRAFREEAIKF-SEEQRFNNFLKALR
.ENFRVLVKQK.ASFEEAS.QLINHI.QFLD.N.T.YF.KS.DCIRAF..EAIKF.S.EQ.FNNFL.AL.
RetrocopyTENFRVLVKQKNASFEEASVQLINHIKQFLDNNGTQYFTKSRDCIRAFQKEAIKF<SKEQCFNNFL*AL*
ParentalEKVESKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKEKPSEDTAAAFEEGGDVEDLL
EKVE.KQLNH.WEIVVQDGITLITKEEASG.SVTAEEAKKFLA.K.KPSEDTAA.FEEG....DLL
RetrocopyEKVEIKQLNHLWEIVVQDGITLITKEEASGRSVTAEEAKKFLAAKVKPSEDTAAVFEEGAYGNDLL

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 133 .75 RPM
SRP051959_heart 0 .00 RPM 98 .21 RPM
SRP051959_kidney 0 .00 RPM 149 .34 RPM
SRP051959_liver 0 .00 RPM 129 .51 RPM
SRP051959_lung 0 .00 RPM 120 .05 RPM
SRP051959_lymph_node 0 .00 RPM 133 .72 RPM
SRP051959_skeletal_muscle 0 .00 RPM 125 .68 RPM
SRP051959_spleen 0 .00 RPM 135 .25 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_2256 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2256 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2256 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000012291 2 retrocopies
retro_cjac_2178, retro_cjac_2256 ,


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