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 symbol: PNPT1
• Ensembl ID: ENSGGOG00000006867
• Aliases: None
• Description: None

Sequence

>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

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1912 was not experimentally validated.

Homology

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

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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,