RetrogeneDB ID: retro_pabe_853

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:63053358..63053674(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM242
• Ensembl ID: ENSPPYG00000017271
• Aliases: None
• Description: Transmembrane protein 242 [Source:UniProtKB/Swiss-Prot;Acc:Q5R987]

Sequence

>retro_pabe_853
GGCTCTGGGACTGGGCAGCTGGCCTCTCTGCTGGAGGCTTCGGGGTCCACGGATGACTGGCTTTTCCTGGTTAAAGGTGG
AATTTTCCTTGGTATTGTTGCTGCAGCAGGAATGCTAGCTGGATTTATTACAACATTATCATTGGCTAAAAAGAAAAGCC
CTGAATGGTTCAATAAGGGAAGTACGGCCACCATCGCATTACCGGAAAGCGGGTCTTCCCTTGCCTTACTGAGCTCTGGG
CTGGGGCTTACTGTATGCATGGTATGGGGTTGGTGTGATTAGCTTCTCAGTCGGGAAAGCTTTAGGAGTTCACAGT

Alignment

ORF - retro_pabe_853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 74.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAGTGQPASGLEAPGSADDRLFLVKGGIFLGTVAAAGMLAGFITTLSLAKKKSPEWFNKGSMATAALPES
          G.GTGQ.AS.LEA.GS.DD.LFLVKGGIFLG.VAAAGMLAGFITTLSLAKKKSPEWFNKGS.AT.ALPES
Retrocopy GSGTGQLASLLEASGSTDDWLFLVKGGIFLGIVAAAGMLAGFITTLSLAKKKSPEWFNKGSTATIALPES

Parental  GSSLALR-ALGWGSLYAWCGVGVISFAVWKALGVHS
          GSSLAL..ALGWG.LYAW.GVGVISF.V.KALGVHS
Retrocopy GSSLALL>ALGWGLLYAWYGVGVISFSVGKALGVHS

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	28.03 RPM
SRP007412_cerebellum	0.12 RPM	36.60 RPM
SRP007412_heart	0.00 RPM	12.97 RPM
SRP007412_kidney	0.00 RPM	16.51 RPM
SRP007412_liver	0.00 RPM	11.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_853 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_853 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1016
Pan troglodytes	retro_ptro_747
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,