RetrogeneDB ID: | retro_ggor_1912 | ||
Retrocopy location | Organism: | Gorilla (Gorilla gorilla) | |
| Coordinates: | 3:4117869..4120180(-) | ||
| 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: | ENSGGOG00000006867 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ggor_1912
CTCTGGCTCCGGCCGCTGAGTGATGGTCCCTTCTGTCTGCCAGGGTGGGATCAGGCACTCATCCAGTTGCAGGTGCGAGC
ACTATTGAGTAGCACAGGGTCTCGAGCTGTGGCCATGGACTTGGGCAACAGGAAGTTAGAAATATCCTCTGGAAAGCTGG
CCAGATTTGCAAATGGCTCTGCTGTAATACAGTCAGGTGACACTGCAGTAATGGCCACAGCAGTCAGTAAAACAAAACCT
TCACCTTCCCAGTTTATGCCTTTGGTGGTTGACTACAGACAAAAGGCTGCTGCAGTAGGTAGAATTCCCACAAACCCTCT
GAGAAGAGAGATTAGTACTTCTGATAAAGAAATTCTTACACGTTGAATAATAGATTGTTCAGTTAGACCTATCTTTCCAG
CTGGCTACTTCTGTGATATACAGGTTCTGTGTAATCTGTTAGCAGTAGATGGTATTAATGAACTTGATGTCCTAGCAATT
AATGGCACCTCTGTAGCCCTCTCATTATCAGATATTCTTTGGAATGGACCTGTTGGGACAGTATGAATAGGAATGACTGA
TGGAGAATGTGTTGTTAACCCAACAAGAAAAGAAATGTCTTCTAGTACTTTAAATGTAGTGGTTGCTGGAGCACCTAAAA
GTCAGATTGTCATGTTGGAAGCCTCTGCAGAGAACATTTTACAGCAGGACTTTTGCCATGCTATCAAAGTGGGAGTGAAA
TATACCCAACAAATAATTCAGGGCATCCAGCAGTTGGTAAAAGAAATTGGTGTTACCAAGAGGACACCTCAGAAGTTATT
TACCCCTTCACAAGAGATTGTGAAACATGCTCATAAACTCACTATGGAGAGACTCTATGCAGTTTTTACAGATTATGAAC
ATGATAAAATTTCCAGAGATGAAGCTGTTAACAAAATAAGATTAGATACAGAGGAACAACTAAAAGAAATATTTCCAGAG
GTCGATCTATATGAGATAATAGAATCCTTCAATATTGTTGCAAAGGAAGTTTTTAGAAGTATTATTTTGAATGAATACAA
AAGTTGCGATGGTCGGGATTTGACTTTACTTAGGAATATAAGTTGTGAGGTAGATATGTTTAAAACCCTTCATAGATCAG
AATTATTTCAAAGAGGACAAACACCCGTGCTTTGTACTGTTACATTTGATTCATTAGAATCCAATATTAAGTTGGATCGA
GTTATAACAACTATAAATGGGATAAAAGATAAAAATTTCATGCTGCACTATGAGTTTCCTCCTTATGCAACTAATGAAAT
TGTCAAAGTCACCGGTATAAATAGAAGAGAACTTGGGCCTGGTGCTCTTGCTGAGAAAGCTTTGTATCCTGTTATTCCCA
AAGATTTTCCTTTTGCCATAAGAGTTACATCTGAAGTCCTAGAGTCAAATGGGTCATCTTCTATGGCATCTGCATGTGGT
GGAAGTTTAGCATTAATGGATTCAGGGCTTCCAATTTAATCTGCTGTCACAGGTGTAGCAATGGGATTGGCCACCAAAAC
CGATCTTGAGAAGGGTGAAATAGATTATCATTTGCTAACAGATATTGTGGTAATTGAAGCTTACAATGGTGACATGGACT
TCAAAATAGCTGGCACTAATAAAGGAATAACTGCATTACAGGCTGATATTAAATTACCTGGAATAACAATGAAAATTGTA
ATGGAGGCTATTCAACAAGCTTCAGTGGCAAAAAGGAGATTTTACAGATCACGAACAAAACTATTTCAAAACCTCAAGCA
TCTAGAAAAGAAAATGGACCTGTTGTAGAAACTGTTCAGGTTCCATTATCAAAATGAGAAAAATTTGTTGGACCAGGTGG
ATATAACTTAAAAAACTTCAGGCTGAAACAGTTGTAACTATTAGTCAGGTGGATGAAGAAACGTTTCCTATGTTTGCACC
AACACCCAGTGCTATGCATGAGGCAAGAGACTTCATTGCTGAAATCTGCAAGGATGATCAGGAGCAGCAATTAGAATTTG
GAGCAGTGTATACCGTCACAATAACTGAAAGCAGAGATACTGGTGTAATGGTAAAATTATATCCAAATATGATTTTGGTA
CTGCTTTATAACAGACAACTTGATCAACGAAATATTAAACATCCTACTGCCCTAGGATTGGAAGTTGGCCGAGAAATTCA
GGTGAAATACTTTGGATGTGACCCAGCTGATGGAAGAATGAGGCTTTCTCACAAAGTGCTTCAGTCTTCAGCTACAACTG
TTGTCAGAACTTTGAATGACAGAAGTAGTATTGTAATGGGAGAACCTATTTCACAGTCATCATCTAATAAT
ORF - retro_ggor_1912 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.7 % |
| Parental protein coverage: | 98.6 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LRLRPLSNGPFLLPGRDRALTQLQVRALWSSAGSRAVAVDLGNRKLEISSGKLARFADGSAVVQSGDTAV |
| L.LRPLS.GPF.LPG.D.AL.QLQVRAL.SS.GSRAVA.DLGNRKLEISSGKLARFA.GSAV.QSGDTAV | |
| Retrocopy | LWLRPLSDGPFCLPGWDQALIQLQVRALLSSTGSRAVAMDLGNRKLEISSGKLARFANGSAVIQSGDTAV |
| Parental | MVTAVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNYLRREIGTSDKEILTSRIIADRSIRPLFPAGYFYD |
| M.TAVSKTKPSPSQFMPLVVDYRQKAAA.GRIPTN.LRREI.TSDKEILT.R.I.D.S.RP.FPAGYF.D | |
| Retrocopy | MATAVSKTKPSPSQFMPLVVDYRQKAAAVGRIPTNPLRREISTSDKEILT-R*IIDCSVRPIFPAGYFCD |
| Parental | TQVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVA |
| .QVLCNLLAVDG.NE.DVLAING.SVALSLSDI.WNGPVG.V.IG..DGE.VVNPTRKEMSSSTLN.VVA | |
| Retrocopy | IQVLCNLLAVDGINELDVLAINGTSVALSLSDILWNGPVGTV*IGMTDGECVVNPTRKEMSSSTLNVVVA |
| Parental | GAPKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKHTHK |
| GAPKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKE.GVTKRTPQKLFTPS.EIVKH.HK | |
| Retrocopy | GAPKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKEIGVTKRTPQKLFTPSQEIVKHAHK |
| Parental | LAMERLYAVFTDYEHDKVDRKQFVGKRVRVSTLKTVREKFPEADPYEIIESFNVVAKEVFRSIVLNEYKR |
| L.MERLYAVFTDYEHDK..R...V.K..R..T.....E.FPE.D.YEIIESFN.VAKEVFRSI.LNEYK. | |
| Retrocopy | LTMERLYAVFTDYEHDKISRDEAVNK-IRLDTEEQLKEIFPEVDLYEIIESFNIVAKEVFRSIILNEYKS |
| Parental | CDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYE |
| CDGRDLT.LRN.SCEVDMFKTLH.S.LFQRGQT.VLCTVTFDSLES.IK.D.VIT.INGIKDKNFMLHYE | |
| Retrocopy | CDGRDLTLLRNISCEVDMFKTLHRSELFQRGQTPVLCTVTFDSLESNIKLDRVITTINGIKDKNFMLHYE |
| Parental | FPPYATNEIGKVTGLNRRELGHGALAEKALYPVIPRDFPFTIRVTSEVLESNGSSSMASACGGSLALMDS |
| FPPYATNEI.KVTG.NRRELG.GALAEKALYPVIP.DFPF.IRVTSEVLESNGSSSMASACGGSLALMDS | |
| Retrocopy | FPPYATNEIVKVTGINRRELGPGALAEKALYPVIPKDFPFAIRVTSEVLESNGSSSMASACGGSLALMDS |
| Parental | VIGVPISSAVAGVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGI |
| ..G.PI.SAV.GVA.GL.TKTD.EKGEI.DY.LLTDI..IE.YNGDMDFKIAGTNKGITALQADIKLPGI | |
| Retrocopy | --GLPI*SAVTGVAMGLATKTDLEKGEI-DYHLLTDIVVIEAYNGDMDFKIAGTNKGITALQADIKLPGI |
| Parental | PIKIVMEAIQQASVA-KKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYN-LKKLQAE |
| ..KIVMEAIQQASVA.KKEILQI.NKTISKP.ASRKENGPVVETVQVPLSK..KFVGPGGYN.LKKLQAE | |
| Retrocopy | TMKIVMEAIQQASVA<KKEILQITNKTISKPQASRKENGPVVETVQVPLSK*EKFVGPGGYN<LKKLQAE |
| Parental | TGVTISQVDEETFSVFAPTPSAMHEARDFITEICKDDQEQQLEFGAVYTATITEISSIQVLIRLFFPMTF |
| T.VTISQVDEETF..FAPTPSAMHEARDFI.EICKDDQEQQLEFGAVYT.TITE.....V...L...M.. | |
| Retrocopy | TVVTISQVDEETFPMFAPTPSAMHEARDFIAEICKDDQEQQLEFGAVYTVTITESRDTGVMVKLYPNMIL |
| Parental | VLIHKHTSAKHSIIKHPTALGLEVGQEIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRSSIVMGE |
| VL...........IKHPTALGLEVG.EIQVKYFG.DPADGRMRLS.KVLQS.ATTVVRTLNDRSSIVMGE | |
| Retrocopy | VLLYNRQLDQRN-IKHPTALGLEVGREIQVKYFGCDPADGRMRLSHKVLQSSATTVVRTLNDRSSIVMGE |
| Parental | PISQSSSNS |
| PISQSSSN. | |
| Retrocopy | PISQSSSNN |
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 | 1 .77 RPM | 19 .04 RPM |
| SRP007412_cerebellum | 1 .54 RPM | 15 .76 RPM |
| SRP007412_heart | 0 .16 RPM | 3 .47 RPM |
| SRP007412_kidney | 1 .72 RPM | 15 .91 RPM |
| SRP007412_liver | 0 .92 RPM | 10 .52 RPM |
| SRP007412_testis | 3 .00 RPM | 37 .40 RPM |
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_1912 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ggor_1912 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2749 |
| Pan troglodytes | retro_ptro_1857 |
| Pongo abelii | retro_pabe_2220 |
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 |
retro_ggor_1912 ,
|
| Pongo abelii | ENSPPYG00000012399 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000011934 | 1 retrocopy |