RetrogeneDB ID:

retro_pabe_2220

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:66172383..66174693(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PNPT1
Ensembl ID:ENSPPYG00000012399
Aliases:PNPT1, PNPASE
Description:polyribonucleotide nucleotidyltransferase 1, mitochondrial [Source:RefSeq peptide;Acc:NP_001125193]


Retrocopy-Parental alignment summary:






>retro_pabe_2220
CTCTGCCTCTGGCCGCTGAGCGATGGTCCCTTTTGTCTGCCAGGGTGGGATCGGGCACTCATCCAGTTGCAGGTGCGAGC
ACTATTGAGTAACACAGGGTCTCGAGCTGTGGCCATGGACTTGGGCAACAGGAAATTAGAAATATCCTCTGGAAAGCTGG
CCAGATTTGCAAGTGGCTCTGCTGTAGTACAGTCAGGTGACACTGCAGTAATGGCCACAGGGGTCAGTAAAACAAAACCT
TCACCTTCCCAGTTTATGCCTTTGGTGGTTGACTACAGACAAAAGGCTGCTGCAGCAGGTAGAATTCCCACAAACCCTCT
GAGAAGAGAGAATAGTACTTCTGATAAAGAAATTCTTACATGTTGAATAATAGATTGTTCAGTTAGACCTATCTTTCCAG
CTGGCTACTTCTGTGATATACAGGTTCTGTGTAATCTGTTAGCAGTAGATGGTATTAATGAGCTTGATGTCCTAGCAATT
AATGGTGCCTCTGTAGCCCTCTTATTATCAGATATTCTTTGGAATGGACCTGTTGGGACAGTATGAATAGGAATGACTGA
TGAAGAATGTGTTGTTAACCCAACAAGAAAAGAAATGGCTTCTAGTACTTTAAATGTAGTGGTTGCTGGAGCACCTAAAA
GTCAGATTGTCATGTTGGAAGCCTCTGCAGAGAACATTTTAGAGCAGGACTTTTGCCACGCTATCAAAGTGGGAGTGAAA
TATACCCAACAAATAATTCAGGGCATCCAGCAGTTGGTAAAAGAAATTGGGGTTACGAAGAGGACACCTCAGAAGTTATT
TACCCCTTCACCAGAGATTGTGAAACATTCTCATAAACTCATTATGGAGAGACTCTATGCAGTTTTTACAGGTTGTGAAC
ATGATAAAATTTCCAGAGATGAAGCTGTTAACAAAATAAGATTAGATACAGAGGAACAACTAAAAGAAATATTTCCAGAG
GTCGATCTATATGAAATAATAGAATCCTTCAATGTTGTTGCAAAGGAAGTTTTTAGAAATATTATTTTGAATGAATACAA
AAGATGTGATGGTTGGGATTTGACTTTACTTAGGAATATAAGTTGTGAGGTAGATATGTTTAAAACCCTTCATAGATCAG
AATTATTTCAAAGAGGACAAACACAGGTGCTTTGTACTGTTATATTTGATTCATTAGAATCCAGTATTAAGTTGGATCGA
GTTATAACAGCTATAAATGGGATAAAAGATAAAAATTTCATGATGCACTATGAGTTTCCTCCTTATGCAACTAAGGAAGT
TGTCAAAGTCACCAGTATAAATAGAGGAGAACTTGGGCTTGGTGCTCTTGCTGAGAAAGCTTTATATCCTGTTATTCCCA
AAGATTTTCCTTTTGCCATAAGAGTTACATCTGAAGTCCTAGAGTCAAATGAGTCATCTTCTATGGCATCTGCATGTGGT
GGAAGTTTAGCATTAATGGATTCAGGGGTTCCAATTTCATCTGCTGTCACAGGTGTAGCAATGGGATTGGCCATCAAAAC
CGATCTTGAGAAGGGCGAAATAGAAGATTATCATTTGCTAACAGATATTCTGGGAATTGAAGATTAGAATGGTGACATGG
ACTTCAAAATAGCTGGCACTAATAAAGGAATAACTGCATTACAGGCTGATATTAAATTACCTGGAATACCAATGAAAATT
GTAATGGAGGCTATTCAACAAGCTTCAGTGGCAAAAAGGAGATTTTACAGATCATGAACAAAACTATTTCAAAACCTCAA
GCATCTAGAAAAGAAAATGGACCTGTTGTAGAAACTGTTCAGGTTCCATTATCAAAACGAGAAAAATTTGTTGGACCAGG
TGGATATAACTTAAAAAACTTCAGGCTGAAGCAGTTGTAACTATTAGTCAGGTGGATGAAGAAATGTTTTCTATATTTGC
ACCAACACCCAGTGCTATGCATGAGGCAAGAGACTTCATTGCTGAAATCTGCAAGGATGATCAGGAGCAGCAATTAGAAT
TTGGAGCAGTGTATACCGCCACAATAACTGAAAGCAGAGATACTGGTGTAATGGTAAAATTATATCCAAATATGATTTTG
GTACTGCTTTTTAAGACACAACTTGATCAACGAAATATTAAACATCCTACTGCCCTAGGATTAGAAGTTGGCCAGAAATT
CAGGTGAAATACTTTGGATGTGACCCAGCTGATGGAAGAATGAGGCTTTCTCATAAAGTGCTTCAGTCTTCAGCTACAAC
TGTTGTCAGAACTTTGAATGACAGAAGTAGTATTGTAATGGGAGAACCTATTTCACAGTCATCATCTAAT

ORF - retro_pabe_2220 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.86 %
Parental protein coverage: 98.47 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLRLRPLSDGPFCLPGRDRALTQLLVRALWSSTGSRAVAVDLGNRKLEISSGKLARFADGSAVVTSGDTAV
L.L.PLSDGPFCLPG.DRAL.QL.VRAL.S.TGSRAVA.DLGNRKLEISSGKLARFA.GSAVV.SGDTAV
RetrocopyLCLWPLSDGPFCLPGWDRALIQLQVRALLSNTGSRAVAMDLGNRKLEISSGKLARFASGSAVVQSGDTAV
ParentalMVTAVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNYLRREIGTSDKEILTSRIIDRSIRPLFPAGYFYDT
M.T.VSKTKPSPSQFMPLVVDYRQKAAAAGRIPTN.LRRE..TSDKEILT..IID.S.RP.FPAGYF.D.
RetrocopyMATGVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNPLRRENSTSDKEILTC*IIDCSVRPIFPAGYFCDI
ParentalQVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGECVVNPTRKEMSSSTLNLVVAG
QVLCNLLAVDG.NE.DVLAINGASVAL.LSDI.WNGPVG.V.IG..D.ECVVNPTRKEM.SSTLN.VVAG
RetrocopyQVLCNLLAVDGINELDVLAINGASVALLLSDILWNGPVGTV*IGMTDEECVVNPTRKEMASSTLNVVVAG
ParentalAPKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKHTHKL
APKSQIVMLEASAENIL.QDFCHAIKVGVKYTQQIIQGIQQLVKE.GVTKRTPQKLFTPSPEIVKH.HKL
RetrocopyAPKSQIVMLEASAENILEQDFCHAIKVGVKYTQQIIQGIQQLVKEIGVTKRTPQKLFTPSPEIVKHSHKL
ParentalAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPQADPYEIIESFNVVAKEVFRNIILNEYKRCD
.MERLYAVFT..EHDK.SRDEAVNKIRLDTEEQLKE.FP..D.YEIIESFNVVAKEVFRNIILNEYKRCD
RetrocopyIMERLYAVFTGCEHDKISRDEAVNKIRLDTEEQLKEIFPEVDLYEIIESFNVVAKEVFRNIILNEYKRCD
ParentalGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFP
G.DLT.LRN.SCEVDMFKTLH.S.LFQRGQTQVLCTV.FDSLES.IK.D.VITAINGIKDKNFM.HYEFP
RetrocopyGWDLTLLRNISCEVDMFKTLHRSELFQRGQTQVLCTVIFDSLESSIKLDRVITAINGIKDKNFMMHYEFP
ParentalPYATNEIGKVTGLNRRELGHGALAEKALYPVIPRDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGV
PYAT.E..KVT..NR.ELG.GALAEKALYPVIP.DFPF.IRVTSEVLESN.SSSMASACGGSLALMDSGV
RetrocopyPYATKEVVKVTSINRGELGLGALAEKALYPVIPKDFPFAIRVTSEVLESNESSSMASACGGSLALMDSGV
ParentalPISSAVAGVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKI
PISSAV.GVA.GL..KTD.EKGEIEDY.LLTDILGIED.NGDMDFKIAGTNKGITALQADIKLPGIP.KI
RetrocopyPISSAVTGVAMGLAIKTDLEKGEIEDYHLLTDILGIED*NGDMDFKIAGTNKGITALQADIKLPGIPMKI
ParentalVMEAIQQASVA-KKEILQIMNKTISKPRTSRKENGPVVETVQVPLSKRAKFVGPGGYN-LKKLQAETGVT
VMEAIQQASVA.KKEILQIMNKTISKP..SRKENGPVVETVQVPLSKR.KFVGPGGYN.LKKLQAE..VT
RetrocopyVMEAIQQASVA<KKEILQIMNKTISKPQASRKENGPVVETVQVPLSKREKFVGPGGYN<LKKLQAEAVVT
ParentalISQVDEETFSVFAPTPSALHEARDFITEICKDDQEQQLEFGAVYTATITEIRDTGVMVKLYPNMTAVLLH
ISQVDEE.FS.FAPTPSA.HEARDFI.EICKDDQEQQLEFGAVYTATITE.RDTGVMVKLYPNM..VLL.
RetrocopyISQVDEEMFSIFAPTPSAMHEARDFIAEICKDDQEQQLEFGAVYTATITESRDTGVMVKLYPNMILVLLF
ParentalNTQLDQRKIRHPTALGLEVGQ-EIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRSSIVMGEPISQ
.TQLDQR.I.HPTALGLEVGQ.EIQVKYFG.DPADGRMRLS.KVLQS.ATTVVRTLNDRSSIVMGEPISQ
RetrocopyKTQLDQRNIKHPTALGLEVGQ<EIQVKYFGCDPADGRMRLSHKVLQSSATTVVRTLNDRSSIVMGEPISQ
ParentalSSSN
SSSN
RetrocopySSSN

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 .06 RPM 8 .68 RPM
SRP007412_cerebellum 0 .12 RPM 15 .93 RPM
SRP007412_heart 0 .00 RPM 10 .69 RPM
SRP007412_kidney 0 .07 RPM 13 .42 RPM
SRP007412_liver 0 .00 RPM 11 .90 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_2220 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2220 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2220 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2749
Pan troglodytes retro_ptro_1857
Gorilla gorilla retro_ggor_1912
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001380351 retrocopy
retro_hsap_2749,
Gorilla gorilla ENSGGOG000000068671 retrocopy
retro_ggor_1912,
Pongo abelii ENSPPYG00000012399 1 retrocopy
retro_pabe_2220 ,
Pan troglodytes ENSPTRG000000119341 retrocopy
retro_ptro_1857,


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