RetrogeneDB ID:

retro_cjac_2178

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:119324651..119326209(+)
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_2178
ATGGTGATGATATCTTTAGAAGGTGAAGATGGGTTGGATGAAATTTATTCCTGCAGTGAGAGTCTGAGAAAACTGTGTGT
CTTCAAGAAAATTGAGAGGCATTTCATTCACTAGCCCTACCGACTGACCATTGGCTCCAATTTTTCTATAAGGATTGCAG
CCTATAAATTGATTTTACAGGAGAGAGTTAAAAGGACTTGGACAGTTGTGGATGCAAAAACCCTCAAAAAAGAAGATATA
TAAAAAGAAACAGTTTATTGCTTAAATGATGATGATGAAACCAAAGTTTTAAAAAAGGATATTATTTAAGGGTTCCACTA
TGGATGTGATATACCTTTCTCTAAAGTGGATGAGGAGCAAATGAAATATAAATTGGAGGGAAGTGCTTCTGTTTTGGAAT
TTTGTAAATCTTCTCAGGTTCAGAGAAGATTCTTCATGGGAAATCAAGTTCTAAATGTTTTTGCAGCAAGAGACGAGGCA
GCAGCAGTTGCACTTTCCTCCCTGATTCATGCTTTGGACGAGTTAGACTTGGTGGCCATAGTTTGCTATGCTTATGACAA
AAGAACTAATCCTCAAGTCAGGGTGACTTTTCCTCATATCAAGCATAACCATGAGTGTTTAGTGTATGTGTAGCTGCCTT
TCATGGAAGACTTGCTGCAATATATGTTTTTATCCCTGAAAAACAGTAAGAACTATGCTCCCACCGAGGCATAGTTGAAT
GCTGTTGATATTTTGATTGACTCCATGAGCTTAGTAAAGAAAGATGAGAAGACAGACATCCTTGAAGACTTGTTTCCAAC
CACCCAAATCCCAAATCCTCTATTTCAGAAATTATTTTGGTGTCTGCTGCACAGAGCTTTACATCCCTGGGAGCCTCTAC
CCCCAATTGCAGCATATTTGGAATATGCTGAATCCTCCCACTGAAATAACAGCGAAATGTCAGATTTCTTTCTCTAAAAT
AAAGATCCTTTTTCCTCTGATTGAAGCCAAGAAAAAGGATCAAGTAACTGCTCAGGACATTTTCCAAGACAACCATGAAG
ATGGACTCACCACTAAAAAATTAAAGACTGAGGAAGGGGGAGCCTACTTCCACATCTCCAGCCTGGCTGAAGGCAGTGTC
ACCTCTGCTGGAAGTGTGAATCCTGCTGAAAACTTCCATGTTCTAGTGAAACATAAGAATGCCAGCTTTGAGGAAGCGAG
TGACCAGCTCATAAAACACATCAAACAGTTTTTGGATAATAATGAAACACCGTATTTTATGAAGAGCATGGACTGCATCA
GAGCCTTCCAGGAAGAAGCCATTAAGTTTTCAGAAGATCAGTGCTTTAACAACTTCCTGAAAGCCCTTTGAAAGAAAGTG
GAAATTAAACAATTAAATCCTTTCTGGAAAATTGTTGTTCAGGATGGAATTACTCTGATCACCAAAGAGGAAGCCTCTGG
AAGATCTGTCACAGCTGAGGAAGCCAAAAAGTTTCTGGCCCCTAAAGAAAAACCGAATGAAGACACAGCAGCCATATTTA
AAGAAGGTGGTGATGTAGATGATTTACTGGACATGATA

ORF - retro_cjac_2178 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.77 %
Parental protein coverage: 71.45 %
Number of stop codons detected: 6
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVV
MVMISLEGEDGLDEIYS.SESLRKLCVFKKIERH.IH.P.RLTIGSN.SIRIAAYK.ILQERVK.TWTVV
RetrocopyMVMISLEGEDGLDEIYSCSESLRKLCVFKKIERHFIH*PYRLTIGSNFSIRIAAYKLILQERVKRTWTVV
ParentalDAKTLKKEDIQKETVYCLNDDDETEILKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSS
DAKTLKKEDI.KETVYCLNDDDET..LK.DII.GF.YG.DI.PFSKVDEEQMKYK.EG...SVL.FCKSS
RetrocopyDAKTLKKEDI*KETVYCLNDDDETKVLKKDII*GFHYGCDI-PFSKVDEEQMKYKLEGSA-SVLEFCKSS
ParentalQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALNDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECL
QVQRRFFMGNQVL.VFAARD.EAAAVALSSLIHAL..LD.VAIV.YAYDKR.NPQV.V.FPHIKHN.ECL
RetrocopyQVQRRFFMGNQVLNVFAARD-EAAAVALSSLIHALDELDLVAIVCYAYDKRTNPQVRVTFPHIKHNHECL
ParentalVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDE-KTNTLEDMFPTTKIPNPRFQ
VYV.LPFMEDL.QYMF.SLKNSK.YAPTEA.LNAVD.LIDSMSL.KKDE.....L...F...K.....F.
RetrocopyVYV*LPFMEDLLQYMFLSLKNSKNYAPTEA*LNAVDILIDSMSLVKKDE>RQTSLKTCFQPPKSQILYFR
ParentalRLFQCLLHRALHPREPLPPIQQHIWNMLNPPTEVTKKSQIPLSKIKTLFPLIEAKKKDQVIAQDVFQDNH
..F.........P....P..Q.HIWNMLNPPTE.T.K.QI..SKIK.LFPLIEAKKKDQV.AQD.FQDNH
RetrocopyNYFGVCCTELYIPGSLYPQLQ-HIWNMLNPPTEITAKCQISFSKIKILFPLIEAKKKDQVTAQDIFQDNH
ParentalEDGPTAKKLKTEEGGAHFSISSLAEGSVTSVGSVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNE
EDG.T.KKLKTEEGGA.F.ISSLAEGSVTS.GSVNPAENF.VLVK.K.ASFEEAS.QLI.HI.QFLD.NE
RetrocopyEDGLTTKKLKTEEGGAYFHISSLAEGSVTSAGSVNPAENFHVLVKHKNASFEEASDQLIKHIKQFLDNNE
ParentalTLYFMKSMDCIRAFREEAIKFSEEQRFNNFLKALREKVESKQLNHFWEIVVQDGITLITKEEASGSSVTA
T.YFMKSMDCIRAF.EEAIKFSE.Q.FNNFLKAL..KVE.KQLN.FW.IVVQDGITLITKEEASG.SVTA
RetrocopyTPYFMKSMDCIRAFQEEAIKFSEDQCFNNFLKAL*KKVEIKQLNPFWKIVVQDGITLITKEEASGRSVTA
ParentalEEAKKFLAPKEKPSEDTAAAFEEGGDVEDLLDMI
EEAKKFLAPKEKP.EDTAA.F.EGGDV.DLLDMI
RetrocopyEEAKKFLAPKEKPNEDTAAIFKEGGDVDDLLDMI

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 .02 RPM 149 .34 RPM
SRP051959_liver 0 .00 RPM 129 .51 RPM
SRP051959_lung 0 .02 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_2178 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2178 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2178 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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