RetrogeneDB ID:

retro_ptro_3077

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:GL393541.1:53848..55926(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000042552
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SUZ12
Ensembl ID:ENSPTRG00000008980
Aliases:None
Description:SUZ12 polycomb repressive complex 2 subunit [Source:HGNC Symbol;Acc:17101]


Retrocopy-Parental alignment summary:






>retro_ptro_3077
GGAGGGGGTGGCAGTTACTCGGCCTCCTCCTCCTCCTCCGCGGCGGCAGCGGCGGGGGCTGCGGTGTTACCGGTGAAGAA
GCCGAAAATGGAGCACGTCCAGGCTGACCACGAGCTTTTCCTCCAGGCCTTTGAGAAGCCAACACAGATCTATAGATTTC
TTCGAACTCGGAATCTCATAGCACCAATATTTTTGCACAGAACTCTTACTTACATGTCTCATCGAAACTCCAGAACAAAC
ATCAAAAGGAAACATTTAAAGTTGATGATATGTTATCAAAAGTAGAGAAAATGAAAGGAGAGCAAGAATCTCATAGCTTG
TCAGCTCATTTGCAGCTTACGTTTACTGGTTTCTTCCACAAAAATGATAAGCCATCACAAAACTCAGAAAATGAACAAAA
TTCTGTTACCCTGGAAGTCCTGCTTGTGAAAGTTTGCCACAAAAAAAGAAAGGATGTAAGTTGTCCAATAAGGCAAGTTC
CCACAGGTAAAAAGCAGGTGCCTTTGAATCCTGACCTCAATCAAACAAAACCCGGAAATTTCCCGTCCCTTGCAGTTCCC
AGTAATGAATTTGAACCTAGTAACAGCCATATGGTGAAGTCTTACTCGTTGCTATTTAGAGTGACTCGTCCAGGAAGAAG
AGAGTTTAATGGAATGATTAATGGAGAAACCAATGAAAATATTGATGTCAATGAAGAGCTTCCAGCCAGAAGAAAACGAA
ATCGTGAGGATGGGGAAAAGACATTTGTTGCACAAATGACAGTATTTGATAAAAACAGGTGCTTACAGCTTTTAGATGGG
GAATATGAAGTAGCCATGCAGGAAATGGAAGAATGTCCAATAAGCAAGAAAAGAGCAACATGGGAGACTATTCTTGATGG
GAAGAGGCTGCCTCCATTCGAAATATTTTCTCAGGGACCTACGTTGCAGTTCACTCTTCGTTGGACAGGAGAGACCAATG
ATAAATTTACGGCTCCTATTGCCAAACCTCTTGCCACTAGAAATTCAGAGAGTCTCCATCAGGAAAACAAGCCTGGTTCA
GTTAAACCTACTCAAACTATTGCTGTTAAAGAATCATTGACTACAGATCTACAAACAAGAAAAGAAAAGGATACTCCAAA
TGAAAACCGACAAAAATTAAGAATATTTTATCAGTTTCTCTATAACAACAATACAAGGCAACAAACTGAAGCAAGAGATG
ACCTGCATTGCCCTTGGTGTACTCTGAACTGCCGCAAACTTTATAGTTTACTCAAGCATCTTAAACTCTGCCATAGCAGA
TTTATCTTCAACTATGTTTATCATCCAAAAGGTGCTAGGATAGATGTTTCTATCAATGAGTGTTATGATGGCTCCTATGC
AGGAAATCCTCAGGATATTCATCGCCAACCTGGATTTGCTTTTAGTCGCAACGGACCAGTTAAGAGAACACCTATCACAC
ATATTCTTGTGTGCAGGCCAAAACGAACAAAAGCAAGCATGTCTGAATTTCTTGAATCTGAAGATGGGGAGGTAGAACAG
CAAAGAACATATAGTAGTGGCCACAATCGTCTGTATTTCCATAGTGATACCTGCTTACCTCTCCGTCCACAAGAAATGGA
AGTAGATAGTGAAGATGAAAAGGATCCTGAATGGCTAAGAGAAAAAACCATTACACAAATTGAAGAGTTTTCTGATGTTA
ATGAAGGGGAGAAAGAAGTGATGAAACTCTGGAATCTCCATGTCATGAAGCATGGGTTTATTGCTGACAATCAAATGAAT
CATGCCTGTATGCTGTTTGTAGAAAATTATGGACAGAAAATAATTAAGAAGAATTTATGTCGAAACTTCATGCTTCATCT
AGTCAGCATGCATGACTTTAATCTTATTAGCATAATGTCAATAGATAAAGCTGTTACCAAGCTCCGTGAAATGCAGCAAA
AATTAGAAAAGGGGGAATCTGCTTCCCCTGCAAATGAAGAAATAACTGAAGAACAAAATGGGACAGCAAATGGATTTAGT
GGAATTAACTCAAAAGAGAAAGCTTTGGAAACAGATAGTGTCTCAGGGGTTTCAAAACAGAGCAAAAAACAAAAACTC

ORF - retro_ptro_3077 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.99 %
Parental protein coverage: 93.78 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGGGGSYSASSSSSAAAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLT
GGGGSYSASSSSSAAAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLT
RetrocopyGGGGSYSASSSSSAAAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLT
ParentalYMSHRNSRTNIKRK-TFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSQNSENEQNSVTLE
YMSHRNSRTNIKRK.TFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSQNSENEQNSVTLE
RetrocopyYMSHRNSRTNIKRK<TFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSQNSENEQNSVTLE
ParentalVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVT
VLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAV.SNEFEPSNSHMVKSYSLLFRVT
RetrocopyVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVPSNEFEPSNSHMVKSYSLLFRVT
ParentalRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQEMEEC
RPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNR.LQLLDGEYEVAMQEMEEC
RetrocopyRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRCLQLLDGEYEVAMQEMEEC
ParentalPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESLHQENKPGSVK
PISKKRATWETILDGKRLPPFE.FSQGPTLQFTLRWTGETNDK.TAPIAKPLATRNSESLHQENKPGSVK
RetrocopyPISKKRATWETILDGKRLPPFEIFSQGPTLQFTLRWTGETNDKFTAPIAKPLATRNSESLHQENKPGSVK
ParentalPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLK
PTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLK
RetrocopyPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLK
ParentalHLKLCHSRFIFNYVYHPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKR
HLKLCHSRFIFNYVYHPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKR
RetrocopyHLKLCHSRFIFNYVYHPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKR
ParentalTKASMSEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSD
TKASMSEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSD
RetrocopyTKASMSEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQIEEFSD
ParentalVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSID
VNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSID
RetrocopyVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHLVSMHDFNLISIMSID
ParentalKAVTKLREMQQKLEKGESASPANEEIPEEQNGTANGFSEINSKEKALETDSVSGVSKQSKKQKL
KAVTKLREMQQKLEKGESASPANEEI.EEQNGTANGFS.INSKEKALETDSVSGVSKQSKKQKL
RetrocopyKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSGINSKEKALETDSVSGVSKQSKKQKL

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
SRP007412_brain_prefrontal_cortex 0 .43 RPM 7 .79 RPM
SRP007412_cerebellum 0 .04 RPM 12 .05 RPM
SRP007412_heart 0 .12 RPM 4 .37 RPM
SRP007412_kidney 0 .03 RPM 6 .96 RPM
SRP007412_liver 0 .07 RPM 2 .88 RPM
SRP007412_testis 0 .53 RPM 20 .66 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_3077 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3077 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3077 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
Pan troglodytes ENSPTRG00000008980 1 retrocopy
retro_ptro_3077 ,


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