RetrogeneDB ID: retro_pabe_1914

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:38166496..38166905(-)
• Located in intron of: ENSPPYG00000011903

Retrocopy information

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

Parental gene information

• Parental gene symbol: COA1
• Ensembl ID: ENSPPYG00000017606
• Aliases: None
• Description: cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21868]

Sequence

>retro_pabe_1914
TGGCAAAAGTATCCAGGAAGCAGGATGCCAGTGCCTCAAGGAAAAAATGCCCCTTTTCGGCAATGTGTTCAGTACTGAGG
GCTTGGCCCTTGTGTATTACCTCATACAAAAGACTTTTTCCAGGGCTTTGTATTACCGGTTGGCATTGGAGCAGGTGCAT
AGCCATCCCAAGGCACAGGGAGCTCTGGGCCCTCCTCTCAACATTCACTGCCTCAAACTCACCAACAAGCACAACTTTGT
GGACATTGCTGATGCCAAGTTGAAGATTCCTAGCTCTGGATCCAAGTCAGAGGGCCATCTCCACGTCAGCTCATCCAGAA
GTGCCCCTTTCAGAGGTGGCACCTTGATGAGGTCTTCCTAGAGCCCAAGGATGGCCAGCAGATTCCCATGTTCAAGCTCA
GTGGGGAGA

Alignment

ORF - retro_pabe_1914 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.35 %
• Parental protein coverage: 97.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WQKYAGSRRSMPLGARI-LFHSVFCAGGFAIVYYLVQKFHSRGLYYKLAVEQLQSHPEAQEALGPPLNIH
          WQKY.GSR...P.G....LF..VF...G.A.VYYL.QK..SR.LYY.LA.EQ..SHP.AQ.ALGPPLNIH
Retrocopy WQKYPGSRMPVPQGKNA>LFGNVFSTEGLALVYYLIQKTFSRALYYRLALEQVHSHPKAQGALGPPLNIH

Parental  YLKLIDRENFVDIADAKLKIPVSGSKSEGLLYIHSSRGG-PFQRWHLDEVFLELKD-VSRFLCSSSVGK
          .LKL....NFVDIADAKLKIP.SGSKSEG.L...SSR...PFQRWHLDEVFLE.KD..SRF.CSSSVG.
Retrocopy CLKLTNKHNFVDIADAKLKIPSSGSKSEGHLHVSSSRSA<PFQRWHLDEVFLEPKD>ASRFPCSSSVGR

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	14.82 RPM
SRP007412_cerebellum	0.00 RPM	15.20 RPM
SRP007412_heart	0.00 RPM	11.74 RPM
SRP007412_kidney	0.03 RPM	29.40 RPM
SRP007412_liver	0.00 RPM	9.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1914 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1914 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1914 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2595
Pan troglodytes	retro_ptro_1520
Gorilla gorilla	retro_ggor_1624
Callithrix jacchus	retro_cjac_656

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009377	1 retrocopy	retro_amel_1871,
Canis familiaris	ENSCAFG00000031110	1 retrocopy	retro_cfam_2115,
Callithrix jacchus	ENSCJAG00000007826	1 retrocopy	retro_cjac_656,
Homo sapiens	ENSG00000106603	1 retrocopy	retro_hsap_2595,
Gorilla gorilla	ENSGGOG00000034928	1 retrocopy	retro_ggor_1624,
Macaca mulatta	ENSMMUG00000019023	1 retrocopy	retro_mmul_653,
Mustela putorius furo	ENSMPUG00000018149	1 retrocopy	retro_mputfur_1572,
Nomascus leucogenys	ENSNLEG00000003316	1 retrocopy	retro_nleu_1527,
Pongo abelii	ENSPPYG00000017606	1 retrocopy	retro_pabe_1914 ,
Pan troglodytes	ENSPTRG00000019125	1 retrocopy	retro_ptro_1520,