RetrogeneDB ID:

retro_cjac_562

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:81479848..81481378(-)
Located in intron of:ENSCJAG00000004536
Retrocopy
information
Ensembl ID:ENSCJAG00000004586
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SH3KBP1
Ensembl ID:ENSCJAG00000005449
Aliases:None
Description:SH3-domain kinase binding protein 1 [Source:HGNC Symbol;Acc:13867]


Retrocopy-Parental alignment summary:






>retro_cjac_562
GTGGAGGCCATAGTGGAGTTTGACTACCAGGCCCAGCACGACGATGAGCTGACAATCAGCTTGGATGGCATCATCACCAA
CATCAGGAAGGAGGATGGAGGCTGGTGGGAGGGACAGATCAACGGCTGGAGAGGTTTGTTGTCTGACAACTTTGTAAGAG
AAATAAAGAAAGAGATGAAGAAAGACCCTCTCGCCAATAAAGCTCCAGAAAAGCCCATGCATGAAGTGCCCAGTGGAAAC
TCTTTGCTGTCTTCTGAGACGATTTTAAAAGAACCAATAAGAGAGGCGAGCGACTGAGGCGCCAGTGTCAGGTAGCATTC
AGCTACCTGCCCCAGAATGATGATGAACTTGAGCTGAAAATTGGCGACATCGAAGAGGTGGTAGGAGAGGTAGAGGAAGG
ATGGTGGGAAGGTGTTCTCAACGGGAAGACTGGAATGTTTCCTTCCAACTTCATCAAGGAGTTGTCAGGGGAGTCGGATG
AGCTTGGCATTTCCCAGGATGAGCAGCTGTCCAAGTCAAGTTTAAGGGAAACCACAGGCTCCGAGAGTGATGGGGGTGAC
TCAAGCAGCACCAGGTCTGAAGGTGCCAATGGGACAGTGGCAACTGCAGCAATCCAGCCCAAGAAAGTTAAAGGAGTGGG
CTTTGGAGACATTTCAAAGACAAGCCAATCAAACTAAGACCAAGATCAATTGAAGTAGAAAATGACTTTCTGCCGGTGGA
AAAGACTATTGGGAAGAAGCTACCTGCAACTAAGCAACTCCAGACTCATCAAAAACAGAAATGGACAGCAGGACAAAGAG
CAAGGATTACTGCAAAGTAATATTTCCATATGAGGCACAGAATGATGAATTGACAATCAAAGAAGGAGATATAGTCATTC
TCATCAATAGGGACTGCATTGACATAGGGTGGTGGGAAGGAGAGCTGAACGGCAGACGAGGCATGTTCCCTGATAACTTT
GTGAAGTTACTTCCACCGGACTTTGAAAAGGAGGGGAATAGACCCAAGAAGCCACCACCTCCATCCGCTCCTGTCATCAA
ACAAGGGGCAGGTACCACTGAGAGAAAACATGAACTTAAAAAGATACCTCCTGAAAGACCAGAAATGCTTCCCAACAGAA
CAGAAGAAAAAGAAAGACCAGAGAGAGAGAGAGAGCCAAAACTGGATTTACAGAAGTCCTCCGTTCCTGACATACCGTCA
AAAAAGCCTTGGCCACCTAAGACCAATTCTCTCAGCAGACCTGGTGCACTGCCCCCAAGAAGGCCAGAGCGACCGGTGGG
TCCACTGACACACACCAGGGGTGACCGTCCAAAGATTGACTTGGTGGGCAGTTCGCTTTCTGGCATCCTGGACAAAGATC
TCTCGGACCTCAGCAATGACATCGACCTAGAAGGTTTTGACTCCGTGATGTCATCTACTGAGAAACTCAGTCATCCGACC
ACAAGAAGACCAAAAGCTATGGGGAGGCGGCCTCCATCCCAGTCCCTCACATCTGTGTCGGACAACAAAGCATCCCTGCC
ACCCACTCCG

ORF - retro_cjac_562 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.29 %
Parental protein coverage: 93.74 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKKEMKKDPLANKAPE
VEAIVEFDYQAQHDDELTIS...IITNIRKEDGGWWEGQING.RGL..DNFVREIKKEMKKDPLANKAPE
RetrocopyVEAIVEFDYQAQHDDELTISLDGIITNIRKEDGGWWEGQINGWRGLLSDNFVREIKKEMKKDPLANKAPE
ParentalKPMHEVPSGNSLLSSETIL-RTNKRGERRRRR-CQVAFSYLPQNDDELELKVGDIIEVVGEVEEGWWEGV
KPMHEVPSGNSLLSSETIL.........R.RR.CQVAFSYLPQNDDELELK.GDI.EVVGEVEEGWWEGV
RetrocopyKPMHEVPSGNSLLSSETIL<KRTNKRGERLRRQCQVAFSYLPQNDDELELKIGDIEEVVGEVEEGWWEGV
ParentalLNGKTGMFPSNFIKELSGESDELGISQDEQLSKSSLRETTGSESDGGDSSSTKSEGANGTVATAAIQPKK
LNGKTGMFPSNFIKELSGESDELGISQDEQLSKSSLRETTGSESDGGDSSST.SEGANGTVATAAIQPKK
RetrocopyLNGKTGMFPSNFIKELSGESDELGISQDEQLSKSSLRETTGSESDGGDSSSTRSEGANGTVATAAIQPKK
ParentalVKGVGFGDI-FKDKPIKLRPRSIEVENDFLPVEKTIGKKLPATT-ATPDSSKTEMDSRTKSKDYCKVIFP
VKGVGFGDI.FKDKPIKLRPRSIEVENDFLPVEKTIGKKLPAT..ATPDSSKTEMDSRTKSKDYCKVIFP
RetrocopyVKGVGFGDI<FKDKPIKLRPRSIEVENDFLPVEKTIGKKLPATK<ATPDSSKTEMDSRTKSKDYCKVIFP
ParentalYEAQNDDELTIKEGDIVTLINKDCIDVGWWEGELNGRRGVFPDNFVKLLPPDFEKEGNRPKKPPPPSAPV
YEAQN.DELTIKEGDIV.LIN.DCID.GWWEGELNGRRG.FPDNFVKLLPPDFEKEGNRPKKPPPPSAPV
RetrocopyYEAQN-DELTIKEGDIVILINRDCIDIGWWEGELNGRRGMFPDNFVKLLPPDFEKEGNRPKKPPPPSAPV
ParentalIKQGAGTTERKHELKKIPPERPEMLPNRTEEKERP--EREPKLDLQKPSVPAIPPKKPRPPKTNSLSRPG
IKQGAGTTERKHELKKIPPERPEMLPNRTEEKERP..EREPKLDLQK.SVP.IP.KKP.PPKTNSLSRPG
RetrocopyIKQGAGTTERKHELKKIPPERPEMLPNRTEEKERPEREREPKLDLQKSSVPDIPSKKPWPPKTNSLSRPG
ParentalALPPRRPERPVGPLTHTRGDGPKIDLAGSSLSGILDKDLSDRSNDIDLEGFDSVVSSTEKLSHPTTSRPK
ALPPRRPERPVGPLTHTRGD.PKIDL.GSSLSGILDKDLSD.SNDIDLEGFDSV.SSTEKLSHPTT.RPK
RetrocopyALPPRRPERPVGPLTHTRGDRPKIDLVGSSLSGILDKDLSDLSNDIDLEGFDSVMSSTEKLSHPTTRRPK
ParentalATGRRPPSQSLTSSSLSSPDIFDSP
A.GRRPPSQSLTS.S.........P
RetrocopyAMGRRPPSQSLTSVSDNKASLPPTP

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 .11 RPM 4 .90 RPM
SRP051959_heart 0 .51 RPM 6 .75 RPM
SRP051959_kidney 0 .20 RPM 7 .01 RPM
SRP051959_liver 0 .06 RPM 2 .58 RPM
SRP051959_lung 0 .91 RPM 15 .86 RPM
SRP051959_lymph_node 0 .89 RPM 23 .63 RPM
SRP051959_skeletal_muscle 0 .11 RPM 2 .47 RPM
SRP051959_spleen 0 .42 RPM 15 .65 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_562 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_562 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_562 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 ENSCJAG00000005449 2 retrocopies
retro_cjac_3599, retro_cjac_562 ,


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