RetrogeneDB ID:

retro_cjac_2573

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:5:140852043..140853090(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000019391
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SHC1
Ensembl ID:ENSCJAG00000009236
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2573
GCTGGAATGCCAGTCACTCTCACCATCTCCACCAGCAGTCTCAACCTCATGGCCACAGACTGCAAGCAGATCATCGCCAA
CCACCACGTGCAATCTATCTCATTTGCATCCGGCGGGGATCCGGACACAGCTGAGTATGTCGCCTATGTTGCCAAAGACC
CTGTGAATCAGAGAGCCTGCCACATTCTGGAGTGTCCTGAAGGGCTTGCCCAGGATGTTATCAGCACCATTGGCCAGGCC
TTCGAGTTGCGCTTCAAACAATACCTCAGGAACCCACCCAAACTGGTCCCCCCCCATGACAGGATGGCTGGCTTTGATGG
CTCAGCTTGGGATGAAGAGGAGGAAGAGCCACCTGACCATCAGCACTATGACTTCCCAAGGGAAGGAATCCCCTCTTGGG
GGGGTAGTAGACATGAGGCTTCAGGAAGGAGCCACTCTACTCGCTGCCCAGACCCCCAGCCACTTGGGAGCTACACTGCC
TATAGGACAGCCTGTTGGGGGAGATCCAGAAGTCCGCAAACAGATGCCACTTCCACCACCCTGTCCAGCAGGCGGAGAGC
CCTTTGATGATCCCTCCTACCGCAACGTCCAGAACCTAGACAAGGCCCAGCAAGCAGGGGGTGGTGCTGGGCCCCCCAAT
CCTGCCATCAATGGCAGCGTGCCCCAGGACCTATTTGACATGAAGCCCTTTGAAGATGTTCTTCGGGTGCCTCCACCTCC
CCAGTCGGTGACCATGGCTGAGCAGCTCCGAGGGGAGCCCTGGTTTCATGGGAAGCTGAGCCGGCGGGAGGCTGAGGCAC
TGCTGCAGCTCAATGGGACTTCCTGGTGCGGGAGAGCACGACCACACCTGGCCAGTATGTGCTCACTGGCTTGCAGAGTG
GGCAGCCCAAGCATCTGCTACTGATGGACCCTGAGGGTGTGGTATGGACAAAGGATCACCACTTTGAGAGTGTCAGTCAC
CTCATCAGCTACCACACGGACAATCACTTGCCCATCATCTCTGCGGGCAGCGAACTGTGTCTACAGCAACCTGTGGAGCG
GAAACTG

ORF - retro_cjac_2573 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.18 %
Parental protein coverage: 60.66 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAGMPITLTISTSSLNLMAADCKQIIANHHMQSISFASGGDPDTAEYVAYVAKDPVNQRACHILECPEGLA
AGMP.TLTISTSSLNLMA.DCKQIIANHH.QSISFASGGDPDTAEYVAYVAKDPVNQRACHILECPEGLA
RetrocopyAGMPVTLTISTSSLNLMATDCKQIIANHHVQSISFASGGDPDTAEYVAYVAKDPVNQRACHILECPEGLA
ParentalQDVISTIGQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQYYNDFP-GKEPPLGGVVDM
QDVISTIGQAFELRFKQYLRNPPKLV.PHDRMAGFDGSAWDEEEEEPPDHQ.Y.DFP.GKE.PLGGVVDM
RetrocopyQDVISTIGQAFELRFKQYLRNPPKLVPPHDRMAGFDGSAWDEEEEEPPDHQHY-DFP>GKESPLGGVVDM
ParentalRLREGATPPTAQTPSHLGATLPIGQPVGGDPEVRKQMPLPPPCPAGRELFDDPSYVNVQNLDKARQAGGG
RL.EGAT...AQTPSHLGATLPIGQPVGGDPEVRKQMPLPPPCPAG.E.FDDPSY.NVQNLDKA.QAGGG
RetrocopyRLQEGATLLAAQTPSHLGATLPIGQPVGGDPEVRKQMPLPPPCPAGGEPFDDPSYRNVQNLDKAQQAGGG
ParentalAGPPNPAINGSAPRDLFDMKPFEDALRVPPPPQSVTMAEQLRGEPWFHGKLSRREAEALLQLNG-DFLVR
AGPPNPAINGS.P.DLFDMKPFED.LRVPPPPQSVTMAEQLRGEPWFHGKLSRREAEALLQLNG.DFLVR
RetrocopyAGPPNPAINGSVPQDLFDMKPFEDVLRVPPPPQSVTMAEQLRGEPWFHGKLSRREAEALLQLNG<DFLVR
ParentalESTTTPGQYVLTGLQSGQPKHLLLVDPEGVVRTKDHRFESVSHLISYHMDNHLPIISAGSELCLQQPVER
ESTTTPGQYVLTGLQSGQPKHLLL.DPEGVV.TKDH.FESVSHLISYH.DNHLPIISAGSELCLQQPVER
RetrocopyESTTTPGQYVLTGLQSGQPKHLLLMDPEGVVWTKDHHFESVSHLISYHTDNHLPIISAGSELCLQQPVER
ParentalKL
KL
RetrocopyKL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .02 RPM 36 .41 RPM
SRP051959_heart 0 .00 RPM 30 .15 RPM
SRP051959_kidney 0 .00 RPM 34 .10 RPM
SRP051959_liver 0 .02 RPM 17 .26 RPM
SRP051959_lung 0 .00 RPM 27 .59 RPM
SRP051959_lymph_node 0 .05 RPM 33 .42 RPM
SRP051959_skeletal_muscle 0 .00 RPM 10 .48 RPM
SRP051959_spleen 0 .00 RPM 28 .91 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2573 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2573 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2573 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000009236 1 retrocopy
retro_cjac_2573 ,
Homo sapiens ENSG000001606911 retrocopy
Nomascus leucogenys ENSNLEG000000115151 retrocopy
Pongo abelii ENSPPYG000000007691 retrocopy
Pan troglodytes ENSPTRG000000013971 retrocopy
Tarsius syrichta ENSTSYG000000113801 retrocopy



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