RetrogeneDB ID: retro_ptro_747

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:26289635..26289959(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM242
• Ensembl ID: ENSPTRG00000018735
• Aliases: None
• Description: transmembrane protein 242 [Source:HGNC Symbol;Acc:17206]

Sequence

>retro_ptro_747
GAGACAGCGGGCTCTGGTACTGGGCAGCCGGCCTCTCTGCTGGAGGCTCCCGGGTCCACGGATGAGCGGCTTTTCCTGGT
TAAAGGTGGAATTTTCCTTGGTACTGTTGCTGCAGCAGGAACGCTAGCTGGATTTATTACAACATTATCATTGGCTAAAA
AGAAAAGCCCTGAATGGTTCAATAAGGGAAGTATGGTCACGACTGCATTACCGGAAAGCGGGTCTTCCCTTGCCTTGCGA
GCTCTGGGCTGCGGCTCACTGTGTGCATGGTGTGGGGTTGGTGTGATTAGCTTCTCAGTCTGGAAAGCTTTAGGGGTTCA
CAGT

Alignment

ORF - retro_ptro_747 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.81 %
• Parental protein coverage: 84.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETAGAATGQPASGLEAPGSTNDRLFLVKGGIFLGTVAAAGMLAGFITTLSLAKKKSPEWFNKGSMATAAL
          ETAG..TGQPAS.LEAPGST..RLFLVKGGIFLGTVAAAG.LAGFITTLSLAKKKSPEWFNKGSM.T.AL
Retrocopy ETAGSGTGQPASLLEAPGSTDERLFLVKGGIFLGTVAAAGTLAGFITTLSLAKKKSPEWFNKGSMVTTAL

Parental  PESGSSLALRALGWGSLYAWCGVGVISFAVWKALGVHS
          PESGSSLALRALG.GSL.AWCGVGVISF.VWKALGVHS
Retrocopy PESGSSLALRALGCGSLCAWCGVGVISFSVWKALGVHS

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	2.65 RPM
SRP007412_cerebellum	0.00 RPM	3.15 RPM
SRP007412_heart	0.00 RPM	4.78 RPM
SRP007412_kidney	0.00 RPM	2.93 RPM
SRP007412_liver	0.00 RPM	2.29 RPM
SRP007412_testis	0.42 RPM	2.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_747 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_747 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1016
Pongo abelii	retro_pabe_853
Macaca mulatta	retro_mmul_812

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009699	1 retrocopy	retro_amel_1551,
Cavia porcellus	ENSCPOG00000022213	1 retrocopy	retro_cpor_160,
Equus caballus	ENSECAG00000016335	1 retrocopy	retro_ecab_898,
Homo sapiens	ENSG00000215712	1 retrocopy	retro_hsap_1016,
Macaca mulatta	ENSMMUG00000011814	1 retrocopy	retro_mmul_812,
Nomascus leucogenys	ENSNLEG00000010676	1 retrocopy	retro_nleu_222,
Otolemur garnettii	ENSOGAG00000007646	1 retrocopy	retro_ogar_946,
Pongo abelii	ENSPPYG00000017271	1 retrocopy	retro_pabe_853,
Pan troglodytes	ENSPTRG00000018735	1 retrocopy	retro_ptro_747 ,