RetrogeneDB ID: retro_ptro_1381

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:58193242..58194562(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000011425
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: XIAP
• Ensembl ID: ENSPTRG00000022247
• Aliases: XIAP, BIRC4
• Description: X-linked inhibitor of apoptosis [Source:HGNC Symbol;Acc:592]

Sequence

>retro_ptro_1381
GGAGATGCCCTGGGGGGCCTTAGCTGCCCTGAAGCGGTAGACAGGTGGCAACGTGGAGGCTCAGCAGTTGACAGACACAA
GAAAGCAGCGCCGAACTGCAGGTTTATCCGCAGCTTTTATTTTGAAAACAGTGCCACGAAACCTGCAAATCCTGGTGTCC
CAAATAGTCAATACCAAGTTGAAAACCATCTGGGAGAGGAAAAGCGTTGTGCTTTAGACAGGCCGTCTGAGACTCGTGCA
GACCGGCTTTTGAGAGCTGGACAGGTGGTGGATAGATCAGACTCCATACACCCGAGGAGCCCCGCCATGCATAGTGAAGA
AGCTGGATTACAGTCGTTTCACAACTGGCCAGCCTCTGCCCACTTGACCCCGAGAGAGCTGGCCAGTGCTGGGTTGTACT
ACACAGGCACTGATGACCAAGGGCAGTGCTTCTGCTGTGGCGGAAAACTGAAAAACTGGGAACCTGGTGATCGTGCCTGG
TCCGAACACGGGAGACATTTTCCTAATTGCTTCTTTATTTTGGGCCACAACGTTAATATTCGAGGTGAATCTGACGTTGC
GAGTTCTGATAGGAATTTCTCAAATTCAACAAGTTCTCCAAGAAATCCATCCATGACGGGTTATGAAGCCCGGCTCATTA
CTTTTGGGACATGGATGTACTTCGTTAACAAAGAGCAGCTTGCAAGAGCTGGATTTTATGCTATAGGTCAAGAGGATAAA
GTACAGTGCTTTCACTGTGGAGGAGGGCTAGCCAACTGGAAGCCCAAGGAAGATCCTTGGGAACAACATGCTAAATGGTA
TCCAGGTTGCAAATATCTGCTAGAAGAGAAGGGACATGAATATATAAACAACATTCATTTAACCCGTTCACTTGAGGGAG
CTCTGGTACAAACTACCAAGAAAACACCATCACTAACTAAAAGAATCAATGATACCATCTTCCCTAATCCTATGCTACAA
GAAGCTATACGAATGGGATTTGATTTCAAGGACGTTAAGAAAATAATGGAGGAAAGAATTCAAACATCTGGGAGCAACTA
TAAAACGCTTGAGGTTCTTGTTGCAGATCTGGTGAGCGCTCAGAAAGATACTACAGAAAATGAATCGAATCAGACTTCAT
TGCAGAGAGAAATCAGCCCTGAAGAGCCGCTAAGGCGTCTGCAAGACGAGAAGCTTTGTAAAATCTGCATGGACAGACAT
ATCGCTGTTGTTTTTATTCCTTGCGGACATCTGGTCACTTGTAAACAATGTGCTGAAGCAGTTGACAGATGTCCCATGTG
CAGCGCAGTCATTGATTTCAAGCAAAGAGTTTTTATGTCT

Alignment

ORF - retro_ptro_1381 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.77 %
• Parental protein coverage: 88.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDTVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLENSATQSTNSGIQNGQYKVENYLGSRNHF
          GD.....SC..AVDRWQ.G.SAV.RH.K..PNCRFI..FY.ENSAT...N.G..N.QY.VEN.LG.....
Retrocopy GDALGGLSCPEAVDRWQRGGSAVDRHKKAAPNCRFIRSFYFENSATKPANPGVPNSQYQVENHLGEEKRC

Parental  ALDRPSETHADYLLRTGQVVDISDTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQ
          ALDRPSET.AD.LLR.GQVVD.SD.I.PR.PAM.SEEA.L.SF.NWP..AHLTPRELASAGLYYTG..DQ
Retrocopy ALDRPSETRADRLLRAGQVVDRSDSIHPRSPAMHSEEAGLQSFHNWPASAHLTPRELASAGLYYTGTDDQ

Parental  VQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSESDAVSSDRNFPNSTNLPRNPSMADYEA
          .QCFCCGGKLKNWEP.DRAWSEH.RHFPNCFF.LG.N.NIR.ESD..SSDRNF.NST..PRNPSM..YEA
Retrocopy GQCFCCGGKLKNWEPGDRAWSEHGRHFPNCFFILGHNVNIRGESDVASSDRNFSNSTSSPRNPSMTGYEA

Parental  RIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQE
          R..TFGTW.Y.VNKEQLARAGFYA.G..DKV.CFHCGGGL..WKP.EDPWEQHAKWYPGCKYLLE.KG.E
Retrocopy RLITFGTWMYFVNKEQLARAGFYAIGQEDKVQCFHCGGGLANWKPKEDPWEQHAKWYPGCKYLLEEKGHE

Parental  YISNIHLTHSLEECLVRTTEKTPSLTRRIDDTIFQNPMVQEAIRMGFSFKDIKKIMEEKIQISGSNYKRL
          YI.NIHLT.SLE..LV.TT.KTPSLT.RI.DTIF.NPM.QEAIRMGF.FKD.KKIMEE.IQ.SGSNYK.L
Retrocopy YINNIHLTRSLEGALVQTTKKTPSLTKRINDTIFPNPMLQEAIRMGFDFKDVKKIMEERIQTSGSNYKTL

Parental  EVLVADLVNAQIKGMQDESSQTSYRKXISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEA
          EVLVADLV.AQ......ES.QTS....IS.EE.LRRLQ.EKLCKICMDR.IA.VF.PCGHLVTCKQCAEA
Retrocopy EVLVADLVSAQKDTTENESNQTSLQREISPEEPLRRLQDEKLCKICMDRHIAVVFIPCGHLVTCKQCAEA

Parental  VDKCPMCYTVITFKQKIFMS
          VD.CPMC..VI.FKQ..FMS
Retrocopy VDRCPMCSAVIDFKQRVFMS

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	0.00 RPM	2.70 RPM
SRP007412_cerebellum	0.00 RPM	5.31 RPM
SRP007412_heart	0.03 RPM	4.98 RPM
SRP007412_kidney	0.03 RPM	7.24 RPM
SRP007412_liver	0.00 RPM	2.23 RPM
SRP007412_testis	56.06 RPM	1.90 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1381 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1381 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1381 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000009878	1 retrocopy	retro_ocun_82,
Pongo abelii	ENSPPYG00000020696	1 retrocopy	retro_pabe_1682,
Pan troglodytes	ENSPTRG00000022247	1 retrocopy	retro_ptro_1381 ,