RetrogeneDB ID: retro_pabe_176

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:66119729..66120833(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000016754
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_176
ATGGTGAACCACGTTATCAAGTGCAAGGCTGCAGTTGCTTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCACCCCTAAAGGCTCATGAAGTTCTTCGAATCAAGATCATTGCCACTGTGGTTTGCCACACCAACGCCTATACCCTGA
GCGGAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGAAAGTGTTGGCGAGGGA
GTTACTAAGCTGAAGGCGGGTGACACCATCATCCCACTTTACATCCCAGAGTGTGGAGAAGGCAAATTTTGTCTAAATCC
TAAAACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAAAGCCAGATGGTACCAGCAGATTTACTTGCA
AAGGAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTGGCTGATATCTCTGTTGCTAAA
ATAGATCCTTTAGCACCTTTGGATAAAGGCTGCCTTCTAGGTTGTGGCATTTCAACTGGTGATGGTGCTGCTGTGAACAC
TGCCAAGGTGGAGCCTGGCTCTGCTTGTGCCGTCTTTGGTCTGGGAGGAGTTGGATTGGCAGTTATCATGGGCTGTAAAG
TGGCTGGTGCATCCTGGATCATTGGTGTGGACATCGATAAAGATAAATTTGCAAGGGCCAAAGAGTTTGGAGCCACTGAA
TGTATTAACCCTCAGGGTTTTAGTAAACCCATCCAGGAAGTGCTCATTGAGATGACTGATGGAGGAGTGGACTATTCCTT
TGAATGTATTAATGTGAAGGTCATGAGAACAGCACTTGAGGCATGTCACAAGGGCTGGGGCGTCAGCATGGTGGTTGGAG
TAGCTGCTTCAGGTCAAGAAATTGCCACTCATCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGGA
GGATGGAAGAGTGTAGAAAGTTTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAGATGAAAGTTGATGAATTTGTGAC
TCACAGTCTGTCTTTTGATGAAATTAACAAAGCCTTTCAACTGATGGATTCTGGAAAGAGCATT

Alignment

ORF - retro_pabe_176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 98.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEV-RIKIIATAVCHTDAYTLSGADPEGCFPVILGHEG
          M.N.VIKCKAAVAWEAGKPLSIEEIEVAP.KAHEV.RIKIIAT.VCHT.AYTLSGADPEGCFPVILGHEG
Retrocopy MVNHVIKCKAAVAWEAGKPLSIEEIEVAPLKAHEVLRIKIIATVVCHTNAYTLSGADPEGCFPVILGHEG

Parental  AGIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTVLH
          AGIVESVGEGVTKLKAGDT.IPLYIP.CGE.KFCLNPKTNLCQKIRVTQGKGL.PDGTSRFTCKGKT.LH
Retrocopy AGIVESVGEGVTKLKAGDTIIPLYIPECGEGKFCLNPKTNLCQKIRVTQGKGLKPDGTSRFTCKGKTILH

Parental  YMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIM
          YMGTSTFSEYTVVADISVAKIDPLAPLDK.CLLGCGISTG.GAAVNTAKVEPGS.CAVFGLGGVGLAVIM
Retrocopy YMGTSTFSEYTVVADISVAKIDPLAPLDKGCLLGCGISTGDGAAVNTAKVEPGSACAVFGLGGVGLAVIM

Parental  GCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEMLIEMTDGGVDYSFECIGNVKVMRAAL
          GCKVAGAS.IIGVDI.KDKFARAKEFGATECINPQ.FSKPIQE.LIEMTDGGVDYSFECI.NVKVMR.AL
Retrocopy GCKVAGASWIIGVDIDKDKFARAKEFGATECINPQGFSKPIQEVLIEMTDGGVDYSFECI-NVKVMRTAL

Parental  EACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHN
          EACHKGWGVS.VVGVAASG.EIAT.PFQLVTGRTWKGTAFGGWKSVES.PKLVSEYMSKK.KVDEFVTH.
Retrocopy EACHKGWGVSMVVGVAASGQEIATHPFQLVTGRTWKGTAFGGWKSVESFPKLVSEYMSKKMKVDEFVTHS

Parental  LSFDEINKAFELMHSGKSI
          LSFDEINKAF.LM.SGKSI
Retrocopy LSFDEINKAFQLMDSGKSI

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	0.17 RPM	53.41 RPM
SRP007412_cerebellum	0.00 RPM	47.91 RPM
SRP007412_heart	0.15 RPM	86.94 RPM
SRP007412_kidney	0.13 RPM	192.42 RPM
SRP007412_liver	0.03 RPM	157.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_176 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_176 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3607
Pan troglodytes	retro_ptro_2438
Gorilla gorilla	retro_ggor_2434

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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,