RetrogeneDB ID: retro_pabe_2513

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:41136800..41137385(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000014685
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACOT7
• Ensembl ID: ENSPPYG00000001945
• Aliases: None
• Description: cytosolic acyl coenzyme A thioester hydrolase [Source:RefSeq peptide;Acc:NP_001126057]

Sequence

>retro_pabe_2513
CCCTGTCGCCTGACGAACGTGGACAAGGTCCTCGAAGTGCCTCTTGTTGTGTATTTCCGGCAGGAGCAGGAGGAGGAGGG
CCAGAAGTGGTACGAAACCCAGAAGCTGGAGTGCATGGAGACCAAGTGGAGGAACGGGGACATCGTCCAGCCAGTCCTCA
ACCCAGAGCCGAACACTGTCAGCTACAGCCAGTCCAGCTTGATCCACCTGATGAGGGCCTTCAGACTGTACCCTGCACAG
CTTCGTGCATGAAGGCGTGACCATGAAGGTCATGGACGAGGTCGCCGGGCATCTTGGCTAGAACGCCACTGCAAGACCAA
CCTCGTCACAGCTTCCATGGAGGCCATTAATTTTCACGACAAGATCAGAAAAGGCTGCATCAAGACCATCTCGGGACGCA
TGACCTTCACGAGCAATAAGTCCGTAGAGATCGAGGTCTTGGTGGACGCCGACTGTGTTGTGGACAGCTCTCAGAAGCGC
TACCGGGCCGCCAGTGTCTTCACTTAAGTGTCGCTGAGCCAGGAAAGCAGGTCGCTGCCCATGCCCCAGCTCGTGCCCGA
GACCCAGGATGAGAAGAAGCGCTTT

Alignment

ORF - retro_pabe_2513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 51.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PLSLKNVDKVLEVPPVVYSRQEQEEEGRKRYEAQKLERMETKWRNGDIVQPVLNPEPNTVSYSQSSLIHL
          P..L.NVDKVLEVP.VVY.RQEQEEEG.K.YE.QKLE.METKWRNGDIVQPVLNPEPNTVSYSQSSLIHL
Retrocopy PCRLTNVDKVLEVPLVVYFRQEQEEEGQKWYETQKLECMETKWRNGDIVQPVLNPEPNTVSYSQSSLIHL

Parental  V-GPSDCTLHGFVHGGVTMKLMDEVA-GIVAA-RHCKTNIVTASVDAINFHDKIRKGCVITISGRMTFTS
          ..GPSDCTLH.FVH.GVTMK.MDEVA.GI.A..RHCKTN.VTAS..AINFHDKIRKGC..TISGRMTFTS
Retrocopy M>GPSDCTLHSFVHEGVTMKVMDEVA>GILAR>RHCKTNLVTASMEAINFHDKIRKGCIKTISGRMTFTS

Parental  NKSMEIEVLVDADPVVDSSQKRYRAASAFFTYVSLSQEGRSLPVPQLVPETEDEKKRF
          NKS.EIEVLVDAD.VVDSSQKRYRAAS..FT.VSLSQE.RSLP.PQLVPET.DEKKRF
Retrocopy NKSVEIEVLVDADCVVDSSQKRYRAASV-FT*VSLSQESRSLPMPQLVPETQDEKKRF

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	0.50 RPM	83.10 RPM
SRP007412_cerebellum	0.97 RPM	71.99 RPM
SRP007412_heart	0.06 RPM	4.00 RPM
SRP007412_kidney	0.03 RPM	18.26 RPM
SRP007412_liver	0.03 RPM	19.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2513 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2513 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3034
Pan troglodytes	retro_ptro_2047

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000157	2 retrocopies	retro_cjac_1229, retro_cjac_457,
Homo sapiens	ENSG00000097021	1 retrocopy	retro_hsap_3034,
Mustela putorius furo	ENSMPUG00000006882	1 retrocopy	retro_mputfur_177,
Nomascus leucogenys	ENSNLEG00000010371	1 retrocopy	retro_nleu_845,
Pongo abelii	ENSPPYG00000001945	1 retrocopy	retro_pabe_2513 ,
Pan troglodytes	ENSPTRG00000000084	1 retrocopy	retro_ptro_2047,