RetrogeneDB ID: retro_pabe_1682

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:54982764..54983723(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XIAP
• Ensembl ID: ENSPPYG00000020696
• Aliases: None
• Description: X-linked inhibitor of apoptosis [Source:HGNC Symbol;Acc:592]

Sequence

>retro_pabe_1682
GCCAGCCTCTGCCCACTTGACCCCAAGAGAGCTGGCTACTACACAGGCACTGATGACCAAGTGCAGTGCTTCTGTTGTGG
CGGAAAACTGAAAAACTGGGAACCTGGTGATTGTGCCTGGTCAGAACACAGGAGACATTTTCCTAATTGCTTCTTTATTT
TGGGCCACAACGTTAATATTCGAGGTGAATCTGATGTTGCGAGTTCTGATAGGAATTTCTCAAATTAACAAATTCGCCAA
GGAATCCATCCATGACAGGTTATGAAGCCCGGCTCATTACTTTTGGGACATGGATGTAGTCCGTTAACAAAGAGCAGCTT
GCAAGAGCTGGATTTTATGCTATAGGTCAAGAGGATAAAGTACAGTGCTTTCATTGTGGAGGAGGGCTAGCCAACTGGAA
GCCCAAGGAAGACCCTTGGGAACAACATGCTAAATGGTATCCAGGCTGCAAGTATCTGCTAGAAGAGAAGGGACATGAAT
ATATAAACAACATTCATTTAACCCGTTCACTTGAGGGATCTCTGGTAAAAACTACCAAGAAAACACCATCACTAACTAAA
AGAATCAGTGATACCATCTTCCCTAATCCTATGCTACAAGAAGCTATACGAATGGGATTCTGTTTCAAGGACATTAAGAA
AATAATGGAGGAAAAAATTTAAACATCTGGGAGCAACTATAAAACGCTTGAGGTTCTTGTTGCAGATCTGGTGAGCACTC
AGAAAGACACTACAGAAAATGAATCCAATCAGACTTCATAGCAGAGAGAGATCAGCCCTGAAGAGCTGCTAAGGCGTCTG
CAAGAGGAGAAGCTTTGTAAAATCTGCATGGACAGACATACCGCTGTCGTTTTTATTCCTTGTGGACATCTGGTCACTTG
TAAACAATGTGCTGAAGCAGTTGACAGATGTCCCATGTGCAGTGCAGTCATTACTTTCAAGCAAAGAGTTTTTATGTCT

Alignment

ORF - retro_pabe_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 62.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AHLTPRELASAGLYYTGIGDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSESDAVSS
          A.L.P.....AG.YYTG..DQVQCFCCGGKLKNWEP.D.AWSEHRRHFPNCFF.LG.N.NIR.ESD..SS
Retrocopy ASLCPLDPKRAG-YYTGTDDQVQCFCCGGKLKNWEPGDCAWSEHRRHFPNCFFILGHNVNIRGESDVASS

Parental  DRNFPN-STNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPTED
          DRNF.N..TN.PRNPSM..YEAR..TFGTW..SVNKEQLARAGFYA.G..DKV.CFHCGGGL..WKP.ED
Retrocopy DRNFSN<LTNSPRNPSMTGYEARLITFGTWM*SVNKEQLARAGFYAIGQEDKVQCFHCGGGLANWKPKED

Parental  PWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTTEKTPSLTRRIDDTIFQNPMVQEAIRMGFS
          PWEQHAKWYPGCKYLLE.KG.EYINNIHLT.SLE..LV.TT.KTPSLT.RI.DTIF.NPM.QEAIRMGF.
Retrocopy PWEQHAKWYPGCKYLLEEKGHEYINNIHLTRSLEGSLVKTTKKTPSLTKRISDTIFPNPMLQEAIRMGFC

Parental  FKDIKKIMEEKIQISGSNYKSLEVLIADLVNAQKDSTQDESSQTSLQKEISTEEQLRRLQEEKLCKICMD
          FKDIKKIMEEKI..SGSNYK.LEVL.ADLV..QKD.T..ES.QTS.Q.EIS.EE.LRRLQEEKLCKICMD
Retrocopy FKDIKKIMEEKI*TSGSNYKTLEVLVADLVSTQKDTTENESNQTS*QREISPEELLRRLQEEKLCKICMD

Parental  RNIAIVFVPCGHLVTCKQCAEAVDKCPMCYTVITFKQKIFMS
          R..A.VF.PCGHLVTCKQCAEAVD.CPMC..VITFKQ..FMS
Retrocopy RHTAVVFIPCGHLVTCKQCAEAVDRCPMCSAVITFKQRVFMS

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	4.26 RPM
SRP007412_cerebellum	0.00 RPM	6.57 RPM
SRP007412_heart	0.00 RPM	3.40 RPM
SRP007412_kidney	0.00 RPM	3.22 RPM
SRP007412_liver	0.00 RPM	3.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1682 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1682 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,