RetrogeneDB ID: retro_pabe_439

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:124388253..124388704(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THAP3
• Ensembl ID: ENSPPYG00000001935
• Aliases: None
• Description: THAP domain containing, apoptosis associated protein 3 [Source:HGNC Symbol;Acc:20855]

Sequence

>retro_pabe_439
CAGGTGAGGGAGAACACAGCCCCTGCCAGTGAGAGAGGAAATGCCAGCTCTTCTCAGAAAGAAAAGGTCCTCCCTGAGGC
GGGGGCCGGAGAGGACAGCCCTGGGAGAAACAGGGACACTGCGCTTGAAGAGCTTCAGTTGCCGCCAAATGCCAAAGGCC
CAATAAAACAGATCTCGCTTTGGAGGCCGCAAGCGGCAGAGGCTGTTGGCCGGCTAGCCGGCCCTGCAGGCTTGAGAAGT
CCCCTCGACAAGCAGCCATCTGATCACAGCTATGCCCTGTTGGACTTAGGTTCCCTGAAGGAAAAAACTCTTCCTCACTG
TGAAGGAAAACTAAAAGCTCCAGAAGCGCTTGCAGTCCCAGAGGCTGGTGAAGCGAAGGATGTCCAGCTGCCTCCGTGCC
TGCAAAGGGCACTGGGGACTCCAGGTCAGACTTGGGCCAGAGCAGCAGAGC

Alignment

ORF - retro_pabe_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 62.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVRENTDPASERGNASSSQKEKVLPEGGAGEDSPGRNMDTALEELQLPPNAEDPVKQVSPRRPQATEAVG
          QVRENT.PASERGNASSSQKEKVLPE.GAGEDSPGRN.DTALEELQLPPNA..P.KQ.S..RPQA.EAVG
Retrocopy QVRENTAPASERGNASSSQKEKVLPEAGAGEDSPGRNRDTALEELQLPPNAKGPIKQISLWRPQAAEAVG

Parental  QPTGPAGLRRPPNKQPSDHSYALLDLDSLK-KKLFLTLKENEKLRKRLQAQRLVMRRMSSRLRACKGHRG
          ...GPAGLR.P..KQPSDHSYALLDL.SLK.KKLFLT.KEN.KL.KRLQ.QRLV.RRMSS.LRACKGH.G
Retrocopy RLAGPAGLRSPLDKQPSDHSYALLDLGSLK>KKLFLTVKEN*KLQKRLQSQRLVKRRMSSCLRACKGHWG

Parental  LRARLGPEQQS
          L..RLGPEQQS
Retrocopy LQVRLGPEQQS

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	4.64 RPM
SRP007412_cerebellum	0.00 RPM	4.50 RPM
SRP007412_heart	0.00 RPM	1.48 RPM
SRP007412_kidney	0.03 RPM	3.94 RPM
SRP007412_liver	0.00 RPM	2.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_439 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_439 has 0 orthologous retrocopies within eutheria group .

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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	ENSG00000041988	1 retrocopy	retro_hsap_198,
Nomascus leucogenys	ENSNLEG00000008620	1 retrocopy	retro_nleu_1846,
Pongo abelii	ENSPPYG00000001935	1 retrocopy	retro_pabe_439 ,
Pan troglodytes	ENSPTRG00000000093	1 retrocopy	retro_ptro_179,