RetrogeneDB ID: retro_ptro_179

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:104993620..104994071(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THAP3
• Ensembl ID: ENSPTRG00000000093
• Aliases: None
• Description: THAP domain containing, apoptosis associated protein 3 [Source:UniProtKB/TrEMBL;Acc:K7AUB3]

Sequence

>retro_ptro_179
CAGGTGAGGGAGAACACACACACTGCCAGTGAGAGAGGAAATGCCAGCTCTTTTCAGAAAGAAAAGGTCCTCCCTGAGGC
GGGGGCTGGAGAGGACAGCCCTGGGAGAAACATGGACACTGCGCTTGAAGAGCTTCAATTGCCCCCAAATGCCAAAGGCC
CCGTAAAACAGATCTCGCCACGGAGGCCGCAAGCAGCAGAGACTGTTGGCCGGCCGGCCGGCCCTGCAGGCTTGAGAAGG
CCCCCCGACAAGCAGCCATCTGATCACAGCTATGCCCTTTTGGACTTAGATTCCCTGAAGAAAAAAACTCTTCCTCACTC
TGAAGGAAAATGAAAAGCTCCAGAAGCGCTTGCAGGCCCAGAGGCTGGTGAAGTGAAGGATGTCCAGCTGCCTCCGTGCC
TGCAAAGGGCACCGGGGACTCCAGGCCAGACTTGGGCCAGAGCAGCAGAGC

Alignment

ORF - retro_ptro_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.74 %
• Parental protein coverage: 62.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVRENTDPANERGNASSSQKEKVLPEAGAGEDSPGRNMDTALEELQLPPNAEGHVKQVSPRRPQATEAVG
          QVRENT..A.ERGNASS.QKEKVLPEAGAGEDSPGRNMDTALEELQLPPNA.G.VKQ.SPRRPQA.E.VG
Retrocopy QVRENTHTASERGNASSFQKEKVLPEAGAGEDSPGRNMDTALEELQLPPNAKGPVKQISPRRPQAAETVG

Parental  RPTGPAGLRRPPSKQPSDHSYALLDLDSLK-KKLFLTLKENEKLRKRLQAQRLVMRRMSSRLRACKGHQG
          RP.GPAGLRRPP.KQPSDHSYALLDLDSLK.KKLFLTLKENEKL.KRLQAQRLV..RMSS.LRACKGH.G
Retrocopy RPAGPAGLRRPPDKQPSDHSYALLDLDSLK>KKLFLTLKENEKLQKRLQAQRLVK*RMSSCLRACKGHRG

Parental  LQARLGPEQQS
          LQARLGPEQQS
Retrocopy LQARLGPEQQS

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	0.02 RPM	13.87 RPM
SRP007412_cerebellum	0.04 RPM	9.54 RPM
SRP007412_heart	0.00 RPM	3.91 RPM
SRP007412_kidney	0.00 RPM	10.46 RPM
SRP007412_liver	0.07 RPM	4.98 RPM
SRP007412_testis	0.63 RPM	3.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_179 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_179 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 ,