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:
| Parental | LRLRPLSDGPFCLPGRDRALTQLLVRALWSSTGSRAVAVDLGNRKLEISSGKLARFADGSAVVTSGDTAV |
| L.L.PLSDGPFCLPG.DRAL.QL.VRAL.S.TGSRAVA.DLGNRKLEISSGKLARFA.GSAVV.SGDTAV | |
| Retrocopy | LCLWPLSDGPFCLPGWDRALIQLQVRALLSNTGSRAVAMDLGNRKLEISSGKLARFASGSAVVQSGDTAV |
| Parental | MVTAVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNYLRREIGTSDKEILTSRIIDRSIRPLFPAGYFYDT |
| M.T.VSKTKPSPSQFMPLVVDYRQKAAAAGRIPTN.LRRE..TSDKEILT..IID.S.RP.FPAGYF.D. | |
| Retrocopy | MATGVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNPLRRENSTSDKEILTC*IIDCSVRPIFPAGYFCDI |
| Parental | QVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGECVVNPTRKEMSSSTLNLVVAG |
| QVLCNLLAVDG.NE.DVLAINGASVAL.LSDI.WNGPVG.V.IG..D.ECVVNPTRKEM.SSTLN.VVAG | |
| Retrocopy | QVLCNLLAVDGINELDVLAINGASVALLLSDILWNGPVGTV*IGMTDEECVVNPTRKEMASSTLNVVVAG |
| Parental | APKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKHTHKL |
| APKSQIVMLEASAENIL.QDFCHAIKVGVKYTQQIIQGIQQLVKE.GVTKRTPQKLFTPSPEIVKH.HKL | |
| Retrocopy | APKSQIVMLEASAENILEQDFCHAIKVGVKYTQQIIQGIQQLVKEIGVTKRTPQKLFTPSPEIVKHSHKL |
| Parental | AMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPQADPYEIIESFNVVAKEVFRNIILNEYKRCD |
| .MERLYAVFT..EHDK.SRDEAVNKIRLDTEEQLKE.FP..D.YEIIESFNVVAKEVFRNIILNEYKRCD | |
| Retrocopy | IMERLYAVFTGCEHDKISRDEAVNKIRLDTEEQLKEIFPEVDLYEIIESFNVVAKEVFRNIILNEYKRCD |
| Parental | GRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFP |
| G.DLT.LRN.SCEVDMFKTLH.S.LFQRGQTQVLCTV.FDSLES.IK.D.VITAINGIKDKNFM.HYEFP | |
| Retrocopy | GWDLTLLRNISCEVDMFKTLHRSELFQRGQTQVLCTVIFDSLESSIKLDRVITAINGIKDKNFMMHYEFP |
| Parental | PYATNEIGKVTGLNRRELGHGALAEKALYPVIPRDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGV |
| PYAT.E..KVT..NR.ELG.GALAEKALYPVIP.DFPF.IRVTSEVLESN.SSSMASACGGSLALMDSGV | |
| Retrocopy | PYATKEVVKVTSINRGELGLGALAEKALYPVIPKDFPFAIRVTSEVLESNESSSMASACGGSLALMDSGV |
| Parental | PISSAVAGVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKI |
| PISSAV.GVA.GL..KTD.EKGEIEDY.LLTDILGIED.NGDMDFKIAGTNKGITALQADIKLPGIP.KI | |
| Retrocopy | PISSAVTGVAMGLAIKTDLEKGEIEDYHLLTDILGIED*NGDMDFKIAGTNKGITALQADIKLPGIPMKI |
| Parental | VMEAIQQASVA-KKEILQIMNKTISKPRTSRKENGPVVETVQVPLSKRAKFVGPGGYN-LKKLQAETGVT |
| VMEAIQQASVA.KKEILQIMNKTISKP..SRKENGPVVETVQVPLSKR.KFVGPGGYN.LKKLQAE..VT | |
| Retrocopy | VMEAIQQASVA<KKEILQIMNKTISKPQASRKENGPVVETVQVPLSKREKFVGPGGYN<LKKLQAEAVVT |
| Parental | ISQVDEETFSVFAPTPSALHEARDFITEICKDDQEQQLEFGAVYTATITEIRDTGVMVKLYPNMTAVLLH |
| ISQVDEE.FS.FAPTPSA.HEARDFI.EICKDDQEQQLEFGAVYTATITE.RDTGVMVKLYPNM..VLL. | |
| Retrocopy | ISQVDEEMFSIFAPTPSAMHEARDFIAEICKDDQEQQLEFGAVYTATITESRDTGVMVKLYPNMILVLLF |
| Parental | NTQLDQRKIRHPTALGLEVGQ-EIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRSSIVMGEPISQ |
| .TQLDQR.I.HPTALGLEVGQ.EIQVKYFG.DPADGRMRLS.KVLQS.ATTVVRTLNDRSSIVMGEPISQ | |
| Retrocopy | KTQLDQRNIKHPTALGLEVGQ<EIQVKYFGCDPADGRMRLSHKVLQSSATTVVRTLNDRSSIVMGEPISQ |
| Parental | SSSN |
| SSSN | |
| Retrocopy | SSSN |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2220 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
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 | ENSG00000138035 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000006867 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000012399 | 1 retrocopy |
retro_pabe_2220 ,
|
| Pan troglodytes | ENSPTRG00000011934 | 1 retrocopy |