RetrogeneDB ID: retro_ptro_1857

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:4066529..4068843(-)
• Located in intron of: ENSPTRG00000014568

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PNPT1
• Ensembl ID: ENSPTRG00000011934
• Aliases: None
• Description: None

Sequence

>retro_ptro_1857
CTGTGGCTCCGGCCGCTAAGCGATGGTCCCTTCTGTCTGCCAGGGTGGGATCGGGCACTCATCCAATTGCAGGTGCGAGC
ACTATTGAGTAGCACAGGGTCTCGAGCTGTGGGCATGGACTTGGGCAACAAGAAGTTAGAAATATCCTCTGGAAAGCTGG
CCAGATTTGCAAATGGCTCTGCTGTAATATAGTCAGGTGACACTGCAGTAATGGCCACAGCAGTCAGTAAAACAAAACCT
TCCCCTTCCCAGTTTATGCCTTTGGTGGTTGACTACAGACAACAGGCTGCTGCAGTAGGTAGAATTCCCACAAACACTCT
GAGAAGAGAGATTAGTACTTCTGATAAAGAAATTCTTACACGTTGAATAGTAGATTGTTCAGTTAGACCTATCTTTCCAG
CTGGCTACTTCTGTGATATACAGGTTCTGTGTAATCTGTTAGCAGTAGATGGTATTAATGAACTTGATGTCCTAGCAATT
AATGGCACCTCTGTAGCCCTTTCATTATCAGATATTCTTTGGAATGGACCTGTTGGGACAGTATGAATAGGAATGGCTGA
TGGAGAATGTGTTGTTAACCCAACAAGAAAAGAAATGTCTTCTAGTACTTTAAATGTAGTGGTTGCTGGAGCACCTAAAA
GTCAGATTGTCATGTTGGAAGCCTCTGCAGAGAACATTTTACAGCAGGACTTTTGCCACACTATCAAAGTGGGAGTGAAA
TATACCCAACAAATAATTCAGGGCATCCAGCAGTTGGTAAAAGAAATTGGTGTTACCAAGAGGACACCTCAGAAGTTATT
TACCCCTTCACAAGAGATTGTGAAACATGCTCATAAACTCACTATGGAGAGACTCTATGCAGTTTTTACAGATTATGAAC
ATGATAAAATTTCCAGAGATGAAGCTGTTAACAAAATAAGATTAGATACAGAGGAACAACTAAAAGAAATATTTCCAGAG
TTCAATCTATATGAGATAATAGAATCCTTCAATACTGTTGCAAAGGAAGTTTTTAGAAGTATTATTTTGAATGAATACAA
AAGATGCGATGGTCGGGATTTGACTTTACTTAGGAATATAAGTTGTGAGGTAGATATGTTTAAAACCCTTCATGGATCAG
AATTATTTCAAAGAGGACAAACACCGGTGCTTTGTACTGTTACATTTGATTCATTAGAATCCAGTATTAAGTTGGATCGA
GTTATAACAACTATAAATGGGATAAAAGATAAAAATTTCATGCTGCACTATGAGTTTCCTCCTTATGCAACTAATGAAAT
TGTCAAAGTCACTGGTATAAATAGAAGAGAACTTGGGCCTGGTGCTCTTGCTGAGAAAGCTTTGTATCCTGTTATTCCCA
AAGATTTTCCTTTCGCCATAAGAGTTACATCTGAAGTCCTAGAGTCAAATGGGTCATCTTCTATGGCATCTGCATGTGGT
GGAAGTTTAGCATTAATGGATTCAGGGCTTCCAATTTAATCTGCTGTCACAGGTGTAGCAATGGGATTGGCCACCAAAAC
CGATCTTGAGAAGGGTGAAATAGAAGATTATCATTTGCTAACAGATATTGTGGTAATTGAAGCTTACAATGGTGACATGG
ACTTCAAAATAGCTGGCACTAGTAAAGGAATAACTGCATTACAGGCTGATATTAAATTACCTGGAATAGCAATGAAAATT
GTAATGGAGGCTATTCAACAAGCTTTAGTGGCAAAAAGGAGATTTTACAGATCATGAACAAAACTATTTCAAAACCTCAA
GCATCTAGAAAAGAAAATGGACCTGTTGTAGAAACTGTTCAGGTTCCATTATCAAAATAAGAAAAATTTGTTGGACCAGG
TGGATATAACTTAAAAAACTTCAGGCTGAAACAGTTGTAACTATTAGTCAGGTGGATGAAGAAACGTTCTCTATATTTGC
ACCAACACCCAGTGCTATGCATGAGGCAAGAGACTTCATTGCTGAAATCTGCAAGGATGATCAGGAGCAGCAATTAGAAT
TTGGAGCAGTGTATACCGCCACAATAACTGAAAGCAGAGATACTGGTGTAATGGTAAAATTATATCCAAATATGATTTTG
GTACTGCTTTATAACACACAACTTGATCAATGAAATATTAAACATCCTACTGCCCTAGGATTAGAAGTTGGCCAAGAAAT
TCAGGTGAAATACTTTGGATGTGACCCAGCTGATGGAAGAATGAGGCTTTCTCACAAAGTGCTTCAGTCTTCAGCTACAA
CTGTTGTCAGAACTTTGAATGACAGAAGTAGTATTGTAATGGGAGAACCTATTTCACAGTTATCATCTAATAAT

Alignment

ORF - retro_ptro_1857 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.98 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRLRPLSDGPFLLPGRDRALTQLQVRALWSSAGSRAVAVDLGNRKLEISSGKLARFADGSAVVQSGDTAV
          L.LRPLSDGPF.LPG.DRAL.QLQVRAL.SS.GSRAV..DLGN.KLEISSGKLARFA.GSAV..SGDTAV
Retrocopy LWLRPLSDGPFCLPGWDRALIQLQVRALLSSTGSRAVGMDLGNKKLEISSGKLARFANGSAVI*SGDTAV

Parental  MVTAVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNYLRREIGTSDKEILTSRIIDRSIRPLFPAGYFYDT
          M.TAVSKTKPSPSQFMPLVVDYRQ.AAA.GRIPTN.LRREI.TSDKEILT..I.D.S.RP.FPAGYF.D.
Retrocopy MATAVSKTKPSPSQFMPLVVDYRQQAAAVGRIPTNTLRREISTSDKEILTR*IVDCSVRPIFPAGYFCDI

Parental  QVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAG
          QVLCNLLAVDG.NE.DVLAING.SVALSLSDI.WNGPVG.V.IG..DGE.VVNPTRKEMSSSTLN.VVAG
Retrocopy QVLCNLLAVDGINELDVLAINGTSVALSLSDILWNGPVGTV*IGMADGECVVNPTRKEMSSSTLNVVVAG

Parental  APKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKHTHKL
          APKSQIVMLEASAENILQQDFCH.IKVGVKYTQQIIQGIQQLVKE.GVTKRTPQKLFTPS.EIVKH.HKL
Retrocopy APKSQIVMLEASAENILQQDFCHTIKVGVKYTQQIIQGIQQLVKEIGVTKRTPQKLFTPSQEIVKHAHKL

Parental  AMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEVFRSIVLNEYKRCD
          .MERLYAVFTDYEHDK.SRDEAVNKIRLDTEEQLKE.FPE...YEIIESFN.VAKEVFRSI.LNEYKRCD
Retrocopy TMERLYAVFTDYEHDKISRDEAVNKIRLDTEEQLKEIFPEFNLYEIIESFNTVAKEVFRSIILNEYKRCD

Parental  GRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFP
          GRDLT.LRN.SCEVDMFKTLHGS.LFQRGQT.VLCTVTFDSLES.IK.D.VIT.INGIKDKNFMLHYEFP
Retrocopy GRDLTLLRNISCEVDMFKTLHGSELFQRGQTPVLCTVTFDSLESSIKLDRVITTINGIKDKNFMLHYEFP

Parental  PYATNEIGKVTGLNRRELGHGALAEKALYPVIPRDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGV
          PYATNEI.KVTG.NRRELG.GALAEKALYPVIP.DFPF.IRVTSEVLESNGSSSMASACGGSLALMDSG.
Retrocopy PYATNEIVKVTGINRRELGPGALAEKALYPVIPKDFPFAIRVTSEVLESNGSSSMASACGGSLALMDSGL

Parental  PISSAVAGVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKI
          PI.SAV.GVA.GL.TKTD.EKGEIEDY.LLTDI..IE.YNGDMDFKIAGT.KGITALQADIKLPGI..KI
Retrocopy PI*SAVTGVAMGLATKTDLEKGEIEDYHLLTDIVVIEAYNGDMDFKIAGTSKGITALQADIKLPGIAMKI

Parental  VMEAIQQASVA-KKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYN-LKKLQAETGVT
          VMEAIQQA.VA.KKEILQIMNKTISKP.ASRKENGPVVETVQVPLSK..KFVGPGGYN.LKKLQAET.VT
Retrocopy VMEAIQQALVA<KKEILQIMNKTISKPQASRKENGPVVETVQVPLSK*EKFVGPGGYN<LKKLQAETVVT

Parental  ISQVDEETFSVFAPTPSAMHEARDFITEICKDDQEQQLEFGAVYTATITEIRDTGVMVKLYPNMTAVLLH
          ISQVDEETFS.FAPTPSAMHEARDFI.EICKDDQEQQLEFGAVYTATITE.RDTGVMVKLYPNM..VLL.
Retrocopy ISQVDEETFSIFAPTPSAMHEARDFIAEICKDDQEQQLEFGAVYTATITESRDTGVMVKLYPNMILVLLY

Parental  NTQLDQRKIKHPTALGLEVGQEIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRSSIVMGEPISQS
          NTQLDQ..IKHPTALGLEVGQEIQVKYFG.DPADGRMRLS.KVLQS.ATTVVRTLNDRSSIVMGEPISQ.
Retrocopy NTQLDQ*NIKHPTALGLEVGQEIQVKYFGCDPADGRMRLSHKVLQSSATTVVRTLNDRSSIVMGEPISQL

Parental  SSNS
          SSN.
Retrocopy SSNN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.09 RPM	11.98 RPM
SRP007412_cerebellum	0.04 RPM	13.08 RPM
SRP007412_heart	0.06 RPM	16.70 RPM
SRP007412_kidney	0.03 RPM	15.48 RPM
SRP007412_liver	0.03 RPM	13.88 RPM
SRP007412_testis	0.11 RPM	30.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1857 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1857 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1857 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2749
Gorilla gorilla	retro_ggor_1912
Pongo abelii	retro_pabe_2220

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138035	1 retrocopy	retro_hsap_2749,
Gorilla gorilla	ENSGGOG00000006867	1 retrocopy	retro_ggor_1912,
Pongo abelii	ENSPPYG00000012399	1 retrocopy	retro_pabe_2220,
Pan troglodytes	ENSPTRG00000011934	1 retrocopy	retro_ptro_1857 ,