RetrogeneDB ID:

retro_pabe_1137

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:89438851..89441484(+)
Located in intron of:ENSPPYG00000006046
Retrocopy
information
Ensembl ID:ENSPPYG00000006047
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM35A
Ensembl ID:ENSPPYG00000002828
Aliases:None
Description:protein FAM35A [Source:RefSeq peptide;Acc:NP_001125252]


Retrocopy-Parental alignment summary:






>retro_pabe_1137
ACAGTTTCTTTAATGTCCGTTGCTGACCCCTGGAAAAAAATTCAGCTTTTATACAGTCAACATTCTTTATATCTGAAGGA
TGAAAAACAGCACAAAAATCTTGAAAACTATGAAGTCCCAGAATCTATTGGTTCTCCAGATCTTAGTGGTCATTTCTTAG
CAAACTGTATGAATAGACATGTTCATGTGAAAGATGACTTACGTACATTCTGTTTCTGAAACACAGAATATAGAATCCCA
GAAGATTCACTCCTTTGGACTGAGTGATGTAACTAGCTCTAATATGCAAATATGTGGATTTAAAAGCACGGTTCTGCATT
TAACTGAAAAGTATCAAAAGCTTCTCAGTGAAAATAAAATTATAGATGAACAGCCTAAACATCAGTCAGATATATGTGGT
CAGAACTTTAACACAAATTTGTTTCAGTTAGGCCACAAATGTGCAGCTATGTTGGATTTGGTTTCTAGTACTAAACAAAT
TAATATAGGGCCTGAAGTGGTACAAAGAGAGTGTGTGCCAACAGAATATCATGAAATACAAAACCAGTGTTTGGGACTAT
TTTCCTTGAACACAGTAGACAAGCCAAGGTCTGACGCAGCAGTTAGGAAGGTCTCAGACCTTAAAATGTCAACTGATACC
GAACTTCTCTGTATAATTACCTCCAGCCAGGTTGCTTTTTTAGCTCAAAAGAAAGATAAAGGGTGGAGTCCTACAAATAA
AGGGAATGTAAACATGGAGACTGAACCAAAGGCAAGTTATGGGGAGATAAGAATACCCGAAGAGAATTCGATTTCAACTT
GATGATTTTACAGAAGCATATGAAAGTGGACAAAAACTAAGCATATTCTCTTGAAACATTTTAGTCCTGTTTGTCCTAAA
ACAGAAAATTAGCCACATTTCACATAAACTCTGATAAAGGTCCTGAAGAAAAATACAGGATCTCAAAGAACTTTTCAGTT
CTGAAGATGAACTGCCACCAAATGAGATACGTATTGAGTTGTGTAGCTCAGGAATACTGTGTTCCCAATTAAATACCTTC
CACAAAAGTGCTATTAAAAGAAGCTGCACCTCTAAAGATAAAGTGGGCCAGTCTGAAGCTCTGTCTAGAGTCCCTCAAAT
AGCTAAGAAAATGAAGTTGATTTTTAATGCAGGAGATTCTGCTGCAGAAATGGATCAGAGGAATGTGTCTGAATTTAAGG
GTATTAAAAAAAGTCATTAATAAAGAACTGATTCTAAAAGCCAAAAGTATCATTGTTTAGTCATGGTGCTATCTCCATGC
CATGTGAAGGAAATAAACATAAAATTCGGACCAAATTCTGGCTCTAAATTGCCTTTAGCAACAGTTACAGTAATTGATCA
ATCAGAAACTAAGAAGGTTTTTCTGTGGAGGACTGCAGCATTTTGGGCATTTACAGTGTTTCTTGGAGATATAATTTTAC
TCGCAGATGTTGTTATTCATGAGGACCAATGGGTTGGCAAGACAGTACTACAATCAACATTTAGCAGTCAGTTATTAAAT
CTTGGGAGTTATTCATCTATTCAGCCTGAAGAATATTCCAGTGTAGTTAGTGATTTGTACTTCAAGACTTACTGGCACAT
GTGTCCTCAAAATATTCGTACCTCAGAGATCTTCCTCCGAGGCAGCCTCAGAGGGTGAACAGTATAGACTTTGTAGAATT
GGAGCACCTTCAGCCTGATGTATTAGTCCACACAATACTAAGAGTTGTTGATTTCACTATACTGACAGAGGCAGTATACA
GTTATAGAGGACAGCAGCAGAAAAAAGGTATGTTAACAGTGGAACAGGCCCAAGATCAACATTATGTGCTTGTATTATGG
GGTCCTGGAGCAGCCTGGTACCCTCAACTTCAAAGGAAAAAAGGTTATATTTGGGAATTTAAATATCTTTTTGTTCAGCG
CAATTACACACTAGAAAACCTAAAATTGCATACAACGCCTTGGCCATCCTGTGAGTGCTTGTTTGATGATGACATAAAGG
CAATTACATTTAAAGCAAAATTTCAAAAAAGTGCACCCTCCTTTGGGAAAATATCAGACTTAGCAACCCACCTAGAGGAT
AAGTGTTCAGGAGTGGTTCTAATTAAAGCCCAGATTTCAGAGCTGTCATTTCCTATTACGGCAGCTCAGAAGATAGCTCT
AAATGCTCACAGTTCTCTGAAGAGTATTTTTTCTTCTCTTCCCAACATCGTATATACTGGCTGCGCAAAATGTGGATTGG
AACTAGAAACAGATGAGAACAGGATCTACAAACAATGTTTTAGCTGCTTGCCATTTACTATGAAGAAAATATACTATAGG
CCAGCCTTAATGACTGTAGTTGATGGAAGACATGATGTCTGCATCCGTGTAGAATCAAAGCTGATAGAGAAGATTCTTCT
CAACATTTCTGCAGACTGCCTCAATAAGAGTGATAGTTCCTTCCTCAGAGATCACCTATGGGATGGTCATGGCAGACCTG
TTCCACTCCTTGTTGGCAGTCAGCGCAGAACCTTGTGTATTAAAGATTCAGAGCCTTTTTGTGTTAGATGAAAACAACTA
TCCATTACAACAAGATTTCTCCCTCCTGGATTTTTATCCTGACATTGTAAAGCATGGAGCCAATGCCCTTCTC

ORF - retro_pabe_1137 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.1 %
Parental protein coverage: 97.23 %
Number of stop codons detected: 3
Number of frameshifts detected: 10


Retrocopy - Parental Gene Alignment:

ParentalTASLMSVADPWKKIHLLYSQHSLYLKDEKQHKNLENYEVPESVGSPDFSGHFLANCMNRHVHVKDD-FVR
T.SLMSVADPWKKI.LLYSQHSLYLKDEKQHKNLENYEVPES.GSPD.SGHFLANCMNRHVHVKDD..V.
RetrocopyTVSLMSVADPWKKIQLLYSQHSLYLKDEKQHKNLENYEVPESIGSPDLSGHFLANCMNRHVHVKDD>YVH
ParentalSVSETQNIESQNIHSSRLSDITSSNMQICGFKSTVPHLTEEERYQKLLSENKIIDEQPKHQSDICGQNFN
SVSETQNIESQ.IHS..LSD.TSSNMQICGFKSTV.HLTE...YQKLLSENKIIDEQPKHQSDICGQNFN
RetrocopySVSETQNIESQKIHSFGLSDVTSSNMQICGFKSTVLHLTE--KYQKLLSENKIIDEQPKHQSDICGQNFN
ParentalTNLFQLGHKCAAMLDLVCSTEQINIGPEVVQRECVSTEYHEIQNQCLGLFSSNAVDKSRSEAAVRKASDL
TNLFQLGHKCAAMLDLV.ST.QINIGPEVVQRECV.TEYHEIQNQCLGLFS.N.VDK.RS.AAVRK.SDL
RetrocopyTNLFQLGHKCAAMLDLVSSTKQINIGPEVVQRECVPTEYHEIQNQCLGLFSLNTVDKPRSDAAVRKVSDL
ParentalKISTDTEFLSIITSSQVAFLAQKKDKGRSPINKGNVNMETEPKASYREIRIPEENSI-QLDGFTEAYEGG
K.STDTE.L.IITSSQVAFLAQKKDKG.SP.NKGNVNMETEPKASY.EIRIPEENSI.QLD.FTEAYE.G
RetrocopyKMSTDTELLCIITSSQVAFLAQKKDKGWSPTNKGNVNMETEPKASYGEIRIPEENSI>QLDDFTEAYESG
ParentalQ-NQAYSLELF-SPVCP-KTENSRI-HINSDKGLEE-HTGSQ-ELFSSEDELPPNEIHIELCSSGILCSQ
Q.N.AYSLE.F.SPVCP.K...S.I.HINSDKG.EE..TGSQ.ELFSSEDELPPNEI.IELCSSGILCSQ
RetrocopyQ>N*AYSLETF>SPVCP>KQKISHI>HINSDKGPEE>NTGSQ>ELFSSEDELPPNEIRIELCSSGILCSQ
ParentalLNTFHKSAIKRSCTSEDEVGQSEALSRVLQVAKKMKLISNGGDSAVEMDQRNVSEFKGIKKTSLIKNCDS
LNTFHKSAIKRSCTS.D.VGQSEALSRV.Q.AKKMKLI.N.GDSA.EMDQRNVSEFKGIKK.......DS
RetrocopyLNTFHKSAIKRSCTSKDKVGQSEALSRVPQIAKKMKLIFNAGDSAAEMDQRNVSEFKGIKKSH**RT-DS
ParentalKSQKYNCLVMVLSPCHVKEINIKFGPNSGSKVPLATVTVIDQSETKKKVFLWRTAAFWAFTVFLGDIILL
KSQKY.CLVMVLSPCHVKEINIKFGPNSGSK.PLATVTVIDQSETKK.VFLWRTAAFWAFTVFLGDIILL
RetrocopyKSQKYHCLVMVLSPCHVKEINIKFGPNSGSKLPLATVTVIDQSETKK-VFLWRTAAFWAFTVFLGDIILL
ParentalTDVVIREDQWVGETVLQSTFSSQLLNLGSYSSIQPEEYSSVVSDV-VLQDLLAYVSSKHSYLRDLPPRQP
.DVVI.EDQWVG.TVLQSTFSSQLLNLGSYSSIQPEEYSSVVSD..VLQDLLA.VSSK.SYLRDLPPRQP
RetrocopyADVVIHEDQWVGKTVLQSTFSSQLLNLGSYSSIQPEEYSSVVSDL<VLQDLLAHVSSKYSYLRDLPPRQP
ParentalQRVNSIDFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAW
QRVNSIDFVELEHLQPDVLVH..LRVVDFTILTEAVYSYRGQ.QKK.MLTVEQAQDQHYVLVLWGPGAAW
RetrocopyQRVNSIDFVELEHLQPDVLVHTILRVVDFTILTEAVYSYRGQQQKKGMLTVEQAQDQHYVLVLWGPGAAW
ParentalYPQLQRKKGYIWEFKYLFVQRNYTLENLELHTTPWSSCECLFDDDIRAITFKAKFQKSAPSFVKIPDLAT
YPQLQRKKGYIWEFKYLFVQRNYTLENL.LHTTPW.SCECLFDDDI.AITFKAKFQKSAPSF.KI.DLAT
RetrocopyYPQLQRKKGYIWEFKYLFVQRNYTLENLKLHTTPWPSCECLFDDDIKAITFKAKFQKSAPSFGKISDLAT
ParentalHLEDKCSGVVLIQAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGCAKCGLELETDENRIYKQC
HLEDKCSGVVLI.AQISEL.FPITAAQKIALNAHSSLKSIFSSLPNIVYTGCAKCGLELETDENRIYKQC
RetrocopyHLEDKCSGVVLIKAQISELSFPITAAQKIALNAHSSLKSIFSSLPNIVYTGCAKCGLELETDENRIYKQC
ParentalFSCLPFTMKKIYYRPALMTVVDGRHDVCIRVESKLIEKILLNISADCLN-RVIVPSSEITYGMVVADLFH
FSCLPFTMKKIYYRPALMTVVDGRHDVCIRVESKLIEKILLNISADCLN.RVIVPSSEITYGMV.ADLFH
RetrocopyFSCLPFTMKKIYYRPALMTVVDGRHDVCIRVESKLIEKILLNISADCLN>RVIVPSSEITYGMVMADLFH
ParentalSLLAVSAEPCVLKIQSLFVLDENSYPLQQDFSLLDFYSDIVKHGADARL
SLLAVSAEPCVLKIQSLFVLDEN.YPLQQDFSLLDFY.DIVKHGA.A.L
RetrocopySLLAVSAEPCVLKIQSLFVLDENNYPLQQDFSLLDFYPDIVKHGANALL

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 .00 RPM 3 .76 RPM
SRP007412_cerebellum 0 .12 RPM 7 .42 RPM
SRP007412_heart 0 .06 RPM 3 .52 RPM
SRP007412_kidney 0 .00 RPM 19 .66 RPM
SRP007412_liver 0 .09 RPM 19 .43 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_1137 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1137 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1137 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1370
Pan troglodytes retro_ptro_941
Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000000171 retrocopy
retro_dnov_2237,
Homo sapiens ENSG000001223761 retrocopy
retro_hsap_1370,
Nomascus leucogenys ENSNLEG000000116523 retrocopies
retro_nleu_1073, retro_nleu_2157, retro_nleu_840,
Pongo abelii ENSPPYG00000002828 1 retrocopy
retro_pabe_1137 ,
Pan troglodytes ENSPTRG000000024651 retrocopy
retro_ptro_941,


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