RetrogeneDB ID:

retro_pabe_697

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:11:56954920..56956770(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BAP1
Ensembl ID:ENSPPYG00000013809
Aliases:None
Description:BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) [Source:HGNC Symbol;Acc:950]


Retrocopy-Parental alignment summary:






>retro_pabe_697
ATGAATAAGGGCTGGCTGGAGCTGGAGAGCGACCCAGGCCTCTTCACCCTGCTCGTGGAAGATTTCGGTGTCAAAGGGGT
GCAAGTGGAGGAGATCTATGACCTTCAGAGCAAATGTCAGGGCCCTGTATATGGATTTATCCTGTTCAAATGGATCGAAG
AGCGCCAGTCCAGGCGAAAGATCTCTATCTTGGTGGATGATACGTCCATGATTGATGATGATATTGTGAATAACATGTTC
TTTGCCCACCAGCTGATACCCAACTCTTGTGCCACTCATGCCTTGCTGAGCGTGCTCCTGAACCGCAGCACCATGGACCT
GGGACCCACCCTGAGTCTCATGAAGGACTTCACCAAGGGCTTCAGCCCTGAGAGCAAAGGATATGCGATTGGCAATGCCC
CGGAGTTGGCCAAGGCACATAATAGCCATGCCAGGCCCGAGCCACGCCACCTCCGTGAGAAGCAGAATGGCCTTAGTGCA
GTGCGGACCATGGAGGCGTTCCACTTTATCAGCTATGTGCCTATCACAGGCCGGCTCTTTGAGCTGGATGGGCTGAAGGT
CTACCCCATTGACCATGGGCCCTGGGGGGAGGACGAGGAGTGGACAGACAAGTCCCGGCGGGTCATCATGGAGCGTATCG
GCCTCGCCACTGCAGGAGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTAT
GAGGCCAGGATGCACGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGCTGATAAGAGTAACACAGCC
AGAGCTGATTTAGACCCACAAGTCTCAAGAGTCACAGCTGCCTGAGGAGTCCAAGTCAGCCAGCAACAAGTCCCCGCTGG
TGCTGGAAGCAAACAGGGCCCCTGCAGCCTCTGAGGGCACCCACACAGATGGTGCAGAGGAGGCAGCTGGTTCATGCGCA
CAAGCCCCATCCCACAGCCCTCCCAACAAACCCAAGCTGGTAGTGAAGCCTCCAGGCAGCAGCCTCAATGGGGTTCCCCC
CAACCCCACTCCCATTGTCCAGCGGCTGCCAGCCTTTCTAGACAATCACAATTATGCCAAGTCCCCCATGCAGGAGGAAG
AAGACCTGGCGGCAGGTGTGGGCTACGGCCGAGTTCCAGTCCGCCCCCCCCAGCAGTACTCAGATGACGAGGATGACTAT
GAGGATGATGAGGAGGATGGCGTGCAGAACACCAACTCTGCCCTTAGGTATAAGGGGAAGAGAACAGGGAAGCCAGGGGC
ATTGAGCGGTTCTGCTGATGGGCAACTCTCAGTGCTGCAGCCCAACACCATCAACGTCTTGGCTGAGAAGCTCAAAGAGT
CCCAGAAGGACCTCTCAGTTCCTCTGTCCATCAAGACTAGCAGCGGGGCTGGGAGTGCAGCTGTCCAGCTGTGGCAGTGC
CCACACACTCGCAGCCCTCACCCACCCCCAGCAATGAGAGTACGGACACGGCCTCTGAGATCGGCAGTGCTTTCAACTCG
CCACTGCGCTCGCCCATCCGCTCGGCCAACCGGACGCGGCCCTCCAGCCCTGTCACCTCCTACATCTCCAAGGTGCTTTT
TGGAGAGGATGACAGCCTGCTGCGTGTTGACTGCATACACTACAACCGTGCTGTCCGTGATCTGGGTCCTGTCATCAGCA
CAGGCCTGCTGCACCTGGCTGAGGATGGGGTGCTGAGTCCCCTGGCGCTGACAGAGGGTAGGAAGGTTTCCTCGCCCTCC
GTCAGACCAATCCAAGGCAGCCAGGGGTCCAGCAGCCCAGTGGAGAAGGAGGTCATGGAAGCCACGGACAGCAGAGAGAA
GACGGGGATG

ORF - retro_pabe_697 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.38 %
Parental protein coverage: 84.36 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFIFLFKWIEERRSRRKVSTLVDDTS
MNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFI.LFKWIEER.SRRK.S.LVDDTS
RetrocopyMNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFI-LFKWIEERQSRRKISILVDDTS
ParentalVIDDDIVNNMFFAHQLIPNSCATHALLSVLLNCSNVDLGPTLSRMKDFTKGFSPESKGYAIGNAPELAKA
.IDDDIVNNMFFAHQLIPNSCATHALLSVLLN.S..DLGPTLS.MKDFTKGFSPESKGYAIGNAPELAKA
RetrocopyMIDDDIVNNMFFAHQLIPNSCATHALLSVLLNRSTMDLGPTLSLMKDFTKGFSPESKGYAIGNAPELAKA
ParentalHNSHARPEPRHLPEKQNGLSAVRTMEAFHFVSYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDKARRVI
HNSHARPEPRHL.EKQNGLSAVRTMEAFHF.SYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDK.RRVI
RetrocopyHNSHARPEPRHLREKQNGLSAVRTMEAFHFISYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDKSRRVI
ParentalMERIGLATAGEPYHDIRFNLMAVVPDRRIKYEARLHVLKVNRQTVLEALQQLIRVTQPELIQTHKSQESQ
MERIGLATAGEPYHDIRFNLMAVVPDRRIKYEAR.HVLKVNRQTVLEALQQLIRVTQPELI.THKSQESQ
RetrocopyMERIGLATAGEPYHDIRFNLMAVVPDRRIKYEARMHVLKVNRQTVLEALQQLIRVTQPELI*THKSQESQ
ParentalLPEESKSASNKSPLVLEANRAPAASEGTHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVPPNP
LPEESKSASNKSPLVLEANRAPAASEGTHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVPPNP
RetrocopyLPEESKSASNKSPLVLEANRAPAASEGTHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVPPNP
ParentalTPIVQRLPAFLDNHNYAKSPMQEEEDLAAGVGRSRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALRYKG
TPIVQRLPAFLDNHNYAKSPMQEEEDLAAGVG..RVPV....QYSDDEDDYEDDEED.VQNTNSALRYKG
RetrocopyTPIVQRLPAFLDNHNYAKSPMQEEEDLAAGVGYGRVPVXXXXQYSDDEDDYEDDEEDGVQNTNSALRYKG
ParentalKGTGKPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLSIPLSIKTSSGAGSPAVAV---PTHSQPSP-
K.TGKPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLS.PLSIKTSSGAGS.AV.....P....P.P.
RetrocopyKRTGKPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLSVPLSIKTSSGAGSAAVQLWQCPHTRSPHP<
ParentalTPSNESTDTASEIGSAFNSPLRSPIRSANPTRPSSPVTSHISKVLFGEDDSLLRVDCIRYNRAVRDLGPV
TPSNESTDTASEIGSAFNSPLRSPIRSAN.TRPSSPVTS.ISKVLFGEDDSLLRVDCI.YNRAVRDLGPV
RetrocopyTPSNESTDTASEIGSAFNSPLRSPIRSANRTRPSSPVTSYISKVLFGEDDSLLRVDCIHYNRAVRDLGPV
ParentalISTGLLHLAEDGVLSPLALTEGGKGSSPSVRPIQGSQGSSSPVEKEVVEATDSREKTGM
ISTGLLHLAEDGVLSPLALTEG.K.SSPSVRPIQGSQGSSSPVEKEV.EATDSREKTGM
RetrocopyISTGLLHLAEDGVLSPLALTEGRKVSSPSVRPIQGSQGSSSPVEKEVMEATDSREKTGM

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 .44 RPM 212 .76 RPM
SRP007412_cerebellum 0 .12 RPM 71 .02 RPM
SRP007412_heart 0 .06 RPM 25 .89 RPM
SRP007412_kidney 0 .20 RPM 73 .85 RPM
SRP007412_liver 0 .06 RPM 30 .08 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_697 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_697 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_697 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
Pongo abelii ENSPPYG00000013809 1 retrocopy
retro_pabe_697 ,




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