RetrogeneDB ID: retro_pabe_359

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:9164370..9165492(-)
• Located in intron of: ENSPPYG00000000075

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADH5
• Ensembl ID: ENSPPYG00000014946
• Aliases: None
• Description: alcohol dehydrogenase 5 (class III), chi polypeptide [Source:HGNC Symbol;Acc:253]

Sequence

>retro_pabe_359
ATGGCGAACCAGGTTATCAAGTGCAAGGCTGCAGTTGCCTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCACCCCCAAAGGCTCGTAAAGTTTGAATCAAGATCATGCCACTGCAGTTTGCCACACCGATGCCTATACCCTGAGCGG
AGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGAAATTGTGGGAAGTGTTGGTGAGGGAGTTA
CTAAGCTGAAGGCGGGTGATAACTGTCATCCCATTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTAA
AACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAGTGCCAGATGGTACCAGCAGATTTACTTGCAAAG
GAAAGACAATTTTACATTACATGAGAACCAGCACATTTTCTGAATGCACAGTTGTGACTGATACCTCTGTTGCTAAAATA
GATTCTTTAGCACCTTTGGATAAAGCCTGCCTTCTAGGTTGTGGCATTTCAACTGGTTATGGTGCTGCTGTGAACACTGT
CAAGGTGGAGCCTGGCTCTGTTTGTGCTGTCTTTGGCCTGGGAGGAGTTGGATTGACAATTATCATGGGCGGTAAAGTGT
CTGGTGCATCCTGGGTCATTGGTGTGGACATCAATCAAGGTAAATTTCCAAGGGCTAAAGAGTTTGAAGCCACTGAATGT
ATGAACCCTCAGGATTTTAGTAAACCCATCCAGGAAGTGCTCATTGAGATGACGGATGGAGGAGTGGACTACTCCTTTGA
ATGTATTAGGGATGTCAAGGTCGTGAGAGCAGCACTTGAGGCATGTCAACAGGGCTGGGGCGTCAGCGTGGTGGTTGCAG
TAGCTGCTTCAGGTCAAGAAATTGCCACTTATCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGGA
GGGTGAAAGAGTGTAGAAAGTGTCCCAAAGTTGGTATCTGAATATATGTCTAAAAAGATAAAAGTTGATGAATTTGTGAC
TCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTGAACTATTGCATTCTGGAAAGAGCATTCGAACTGTTATCAAGA
TT

Alignment

ORF - retro_pabe_359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKII-ATAVCHTDAYTLSGADPEGCFPVILGHEG
          MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKA..V.IKI..ATAVCHTDAYTLSGADPEGCFPVILGHEG
Retrocopy MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKARKV*IKIM<ATAVCHTDAYTLSGADPEGCFPVILGHEG

Parental  AGIVESVGEGVTKLKAGD-TVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTVL
          A.IV.SVGEGVTKLKAGD.TVIP.YIPQCGECKFCLNPKTNLCQKIRVTQGKGL.PDGTSRFTCKGKT.L
Retrocopy AEIVGSVGEGVTKLKAGD>TVIPFYIPQCGECKFCLNPKTNLCQKIRVTQGKGLVPDGTSRFTCKGKTIL

Parental  HYMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVI
          HYM.TSTFSE.TVV.D.SVAKID.LAPLDK.CLLGCGISTGYGAAVNT.KVEPGSVCAVFGLGGVGL..I
Retrocopy HYMRTSTFSECTVVTDTSVAKIDSLAPLDKACLLGCGISTGYGAAVNTVKVEPGSVCAVFGLGGVGLTII

Parental  MGCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEMLIEMTDGGVDYSFECIGNVKVMRAA
          MG.KV.GAS..IGVDIN..KF.RAKEF.ATEC.NPQDFSKPIQE.LIEMTDGGVDYSFECI..VKV.RAA
Retrocopy MGGKVSGASWVIGVDINQGKFPRAKEFEATECMNPQDFSKPIQEVLIEMTDGGVDYSFECIRDVKVVRAA

Parental  LEACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTH
          LEAC..GWGVSVVV.VAASG.EIAT.PFQLVTGRTWKGTAFGG.KSVESVPKLVSEYMSKKIKVDEFVTH
Retrocopy LEACQQGWGVSVVVAVAASGQEIATYPFQLVTGRTWKGTAFGG*KSVESVPKLVSEYMSKKIKVDEFVTH

Parental  NLSFDEINKAFELMHSGKSIRTVVKI
          NLSFDEINKAFEL.HSGKSIRTV.KI
Retrocopy NLSFDEINKAFELLHSGKSIRTVIKI

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	0.06 RPM	53.41 RPM
SRP007412_cerebellum	0.12 RPM	47.91 RPM
SRP007412_heart	0.09 RPM	86.94 RPM
SRP007412_kidney	0.03 RPM	192.42 RPM
SRP007412_liver	0.06 RPM	157.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_359 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_359 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_330
Pan troglodytes	retro_ptro_266
Gorilla gorilla	retro_ggor_354

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013007	1 retrocopy	retro_cfam_14,
Callithrix jacchus	ENSCJAG00000007198	2 retrocopies	retro_cjac_1029, retro_cjac_2933,
Homo sapiens	ENSG00000197894	3 retrocopies	retro_hsap_175, retro_hsap_330, retro_hsap_3607,
Gorilla gorilla	ENSGGOG00000028244	2 retrocopies	retro_ggor_2434, retro_ggor_354,
Myotis lucifugus	ENSMLUG00000002722	1 retrocopy	retro_mluc_1702,
Macaca mulatta	ENSMMUG00000003552	1 retrocopy	retro_mmul_299,
Mustela putorius furo	ENSMPUG00000009642	1 retrocopy	retro_mputfur_1625,
Nomascus leucogenys	ENSNLEG00000013946	3 retrocopies	retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii	ENSPPYG00000014946	3 retrocopies	retro_pabe_176, retro_pabe_359 , retro_pabe_453,
Pan troglodytes	ENSPTRG00000016303	3 retrocopies	retro_ptro_166, retro_ptro_2438, retro_ptro_266,
Sus scrofa	ENSSSCG00000009185	1 retrocopy	retro_sscr_659,
Xenopus tropicalis	ENSXETG00000009304	1 retrocopy	retro_xtro_57,