RetrogeneDB ID:

retro_cjac_1202

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:43379564..43381137(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PITRM1
Ensembl ID:ENSCJAG00000020425
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1202
GAAGGTCTGAATGACCCCCAGATGTCCTTGGTCTTTAAAGGAGTCTGCTTTAATGAGGTGAAGGAAGCATTTACAGACAA
TGAGAGGATATTCTCCCAGCACCTTCAGAACAGACTTCTTCCAGACCACACTTACTCAGTGGTCTCTGGGGGTGATCCAT
TGTACATCCCAGAGCTTACATGGGAGCAAATTAAGCAATTTCATGTCACTCACTATCACTTAAGCTATGCTAGGTTATTC
ATGCATGGTAATTTTCTGTTAGAACAGCATCTGAAACAAATTCATGAGGAAGCACTGAGAAAATTTCAGAAAATTGAACT
GAGCACCACAGTGCCAGTTCAGACACCCTGGGACAAGCCTAAGGAATTCCAGATAACATGTAGCCCATATTCATTTTCTA
CAGATCCCTCTAAACAAACAACCATCAGCATTAACTTCCTATTACCAGACATCATCAACACATTTGAAGAATTCACACTA
AGTCTTCTGTCTTCACTCTTGATTTCTGGGCCCAACTCTCTTTTACAAAGCCTTGATTGAATCTGGCCTTGGCACAGACT
TTTCTCCTGATGTTGGATATAATAGCTAATAAGGGAGGCCTGCTTCAGAGTTGACCTCCAAGGGATTGTGGAGAAAGACA
TAGAGACCATCAGATGAGTCATAAACAAAACAATTGATGAAGTAGTTGAGAAAAGATTTGAAGATGATCAAATTGAAGCT
TTACTTCATAAAATTGAAATACAGATGAAACATCAGTCTGCCAGCTTTGTATTGACTCTGACATCATACATAGCTTCTTG
CTGGAACCATGATGGGAACCCTGTGGAGCTCTTGAAGTGGGAAATCAGTTGGCTAAATTCAGACAGTGCCTGCAGAAAAA
TCCAAAATTTTTACAAGAAAAAGTAAAACAGTATTTTAAGAATAATCAGCATAAGCTGACTTTATCAATGAGTCCAAACG
ACAAGGGTCATGAGAAGCAAGCACAGGCAGAAGCTACAGAGCTCAAGCAGAAGGTTGAGGCTTTGTCCTCCAGAGACAGG
CAGCAGATCTACAAGAAAGGTTTAGAATTACGGACTCAACAAAGCAAACCTCAAAATGCCTCTTGTCTGCCAGTGTTGAA
AGTTTCAGATATTGAGCCCACCATACCTATCAAGAAGTTGGAAGTGGTCCTGACAATTGGAGATATCCCTGTTCAGTACT
GCACCCAGCCCACCAATGGTGTGGTATATTTCTGGGCCTTCTCCAGTCTGAACATGCTCCCTGAGGAGCTGAGCCCCTAG
GTGCCTCTTTTCTGCAGCATCCTCACCAAACTGGGCTGTGGCCTACCTGACTACCAGGAGCAGGCTCAGCAGATAGAACT
GAAGACTGGAGGAATGATCGCTTCTCCCCACGTGCTCCCTGACAACTTGCATATGGATACCTATGAGCAGGGTGTGCTTT
TCTCCTCTCTCTGCCTGTACCGAAACCTGCCAGACAGATGCATTTATGGAGTGAAATATTTAACAACCCATGCTTTGAGG
AAGAAAAAGATTTAAAAGTGCTGGTGAAGATGACTACCATGCATTTCTCTTCC

ORF - retro_cjac_1202 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.81 %
Parental protein coverage: 51.17 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalENPSDPQTPLVFKGVVFNEMKGVFTDNERIFSQHLQNRLLPDHTYSVVSGGDPLCIPELTWEQLKQFHAT
E...DPQ..LVFKGV.FNE.K..FTDNERIFSQHLQNRLLPDHTYSVVSGGDPL.IPELTWEQ.KQFH.T
RetrocopyEGLNDPQMSLVFKGVCFNEVKEAFTDNERIFSQHLQNRLLPDHTYSVVSGGDPLYIPELTWEQIKQFHVT
ParentalHYHPSNARFFTYGNFPLEQHLKQIQEEALSKFQKIEPSTAVPAQTPWDKPREFQITCGPDSLATDPSKQR
HYH.S.AR.F..GNF.LEQHLKQI.EEAL.KFQKIE.ST.VP.QTPWDKP.EFQITC.P.S..TDPSKQ.
RetrocopyHYHLSYARLFMHGNFLLEQHLKQIHEEALRKFQKIELSTTVPVQTPWDKPKEFQITCSPYSFSTDPSKQT
ParentalTVSVSFLLPDITDTFEAFTLSLLSSLLIS-GPNSPFYKALIESGLGTDFSPDVGYNG-YTREAYFSVGLQ
T.S..FLLPDI..TFE.FTLSLLSSLLIS.GP...FYKALIESGLGTDFSPDVGYN....REA.F.V.LQ
RetrocopyTISINFLLPDIINTFEEFTLSLLSSLLIS>GPTL-FYKALIESGLGTDFSPDVGYNS<LIREACFRVDLQ
ParentalGIAEKDIETVRSLVDRTIDEVIEKGFEDERIEALLHKIEIQMKHQSTSFGLTLTSYIASCWNHDGDPVEL
GI.EKDIET.R.....TIDEV.EK.FED..IEALLHKIEIQMKHQS.SF.LTLTSYIASCWNHDG.PVEL
RetrocopyGIVEKDIETIR*VINKTIDEVVEKRFEDDQIEALLHKIEIQMKHQSASFVLTLTSYIASCWNHDGNPVEL
ParentalLK-LGNQLAKFRQCLQENPKFLEEKVKQYFKNNQHKLTLSMRPDDKYREKQAQVEATKLKQKVEALSPRD
LK..GNQLAKFRQCLQ.NPKFL.EKVKQYFKNNQHKLTLSM.P.DK..EKQAQ.EAT.LKQKVEALS.RD
RetrocopyLK<VGNQLAKFRQCLQKNPKFLQEKVKQYFKNNQHKLTLSMSPNDKGHEKQAQAEATELKQKVEALSSRD
ParentalRQQIYEKGLELRTRQSKPQDASCLPALKVSDIEPTIPATELDVVLTAGDIPVQYCSQPTNGMVYFRAFCS
RQQIY.KGLELRT.QSKPQ.ASCLP.LKVSDIEPTIP...L.VVLT.GDIPVQYC.QPTNG.VYF.AF.S
RetrocopyRQQIYKKGLELRTQQSKPQNASCLPVLKVSDIEPTIPIKKLEVVLTIGDIPVQYCTQPTNGVVYFWAFSS
ParentalLNTLPEELRPYVPLFCSVLTKLGCGLLDYREQAQQIELKTGGMSASPHVLPDDSHMDTYEQGVLFSSHCL
LN.LPEEL.P.VPLFCS.LTKLGCGL.DY.EQAQQIELKTGGM.ASPHVLPD..HMDTYEQGVLFSS.CL
RetrocopyLNMLPEELSP*VPLFCSILTKLGCGLPDYQEQAQQIELKTGGMIASPHVLPDNLHMDTYEQGVLFSSLCL
ParentalDRNLSD-MMHLWSEIFNNPCFEEEEHFKVLVKMTAQELAN
.RNL.D..MHLWSEIFNNPCFEEE...KVLVKMT......
RetrocopyYRNLPD<QMHLWSEIFNNPCFEEEKDLKVLVKMTTMHFSS

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 .07 RPM 24 .54 RPM
SRP051959_heart 0 .00 RPM 46 .41 RPM
SRP051959_kidney 0 .07 RPM 32 .66 RPM
SRP051959_liver 2 .01 RPM 36 .45 RPM
SRP051959_lung 0 .07 RPM 29 .12 RPM
SRP051959_lymph_node 0 .02 RPM 35 .39 RPM
SRP051959_skeletal_muscle 0 .20 RPM 62 .00 RPM
SRP051959_spleen 0 .06 RPM 30 .11 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_1202 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1202 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1202 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 ENSCJAG00000020425 1 retrocopy
retro_cjac_1202 ,


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