RetrogeneDB ID: retro_pabe_453

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:149555329..149556456(-)
• Located in intron of: None

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_453
ATGGCAAACCAGGTTATCAAGTGCAAGGCTGCAGCTGCCTGGGAGGCTGGAAAGCGTCTCTCCATAGAATAGATAGAGGT
GGCACCCCCAAAGGCTCATGAAGTTCAAATTGAGATTGTTGCCACCGTGGTTTGCCACAGTGACGCCTATACCCTGAGCA
GAGCTGGTCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGAAATTGTTGGTGAGGGAGTT
ACTAAGCTGAAGGCAGGTGACACTGTCATCTCACTTTGTATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTAA
AACTCACGTTTGCCAGAAGATAAAGTCACACAAGGGAAAGGATTAATGCCAGATGGTACCAGCAGATTTACTTGCAAAGG
AAAGACAATTTTACATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTGGCTGATATCTCTGTTGCCAAAATAG
ATCCTTTAGCACCTTTGGATAAAGTTGGCCTTCTGGGTTGTGGCATTTCAACTGGTTATGGTCCTGCTGTGAACACTGCC
AAGGTGGAGCCTGGCTCTGTTTGTGCCATCTTTGGCCTGGGAGGAGTTGGATCGGGGGTTACCATGGGCTGTAAAGTGAC
TGGTGCATCCCAGATCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCCAAAGAACTTGGAGCCGCTGAATGTG
TTAGTCCTCAGGATTTTAGTAAACCCACCTAGGAAGTGCTCATTGAGATGATGAGCACTGATGGAGGAGTGGACTATTCC
TTTGAATGTACTGGTAATGTGAAGGTCATGAGAGCAGCACTTGAGGCATGTCACCAGGGCTAGGGCACCAACGTGGTGGT
TGGAGTAGCTGCTTCAGGTGAAGAAATTGCCACTCATCCATTCCAGCCGGCAACAGGTTGCACATGGAAAGGCATTGCCT
TTGGAGGATGGAAGAGTATAGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCACAAAGATAAAAGCTGATGAGTTT
ATGACTCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTGAACTCATGCATTCTGGAAAGAGAATTCGAACTGTTGT
CAAGATT

Alignment

ORF - retro_pabe_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
          MANQVIKCKAA.AWEAGK.LSIE.IEVAPPKAHEV.I.I.AT.VCH.DAYTLS.A.PEGCFPVILGHEGA
Retrocopy MANQVIKCKAAAAWEAGKRLSIE*IEVAPPKAHEVQIEIVATVVCHSDAYTLSRAGPEGCFPVILGHEGA

Parental  GIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIR-VTQGKGLMPDGTSRFTCKGKTVLH
          GIVE.VGEGVTKLKAGDTVI.L.IPQCGECKFCLNPKT..CQKI..VTQGKGLMPDGTSRFTCKGKT.LH
Retrocopy GIVEIVGEGVTKLKAGDTVISLCIPQCGECKFCLNPKTHVCQKIK<VTQGKGLMPDGTSRFTCKGKTILH

Parental  YMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIM
          YMGTSTFSEYTVVADISVAKIDPLAPLDKV.LLGCGISTGYG.AVNTAKVEPGSVCA.FGLGGVG..V.M
Retrocopy YMGTSTFSEYTVVADISVAKIDPLAPLDKVGLLGCGISTGYGPAVNTAKVEPGSVCAIFGLGGVGSGVTM

Parental  GCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEMLIEM--TDGGVDYSFECIGNVKVMRA
          GCKV.GAS.IIGVDINKDKFARAKE.GA.EC..PQDFSKP..E.LIEM..TDGGVDYSFEC.GNVKVMRA
Retrocopy GCKVTGASQIIGVDINKDKFARAKELGAAECVSPQDFSKPT*EVLIEMMSTDGGVDYSFECTGNVKVMRA

Parental  ALEACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVT
          ALEACH.G.G..VVVGVAASGEEIAT.PFQ..TG.TWKG.AFGGWKS.ESVPKLVSEYMS.KIK.DEF.T
Retrocopy ALEACHQG*GTNVVVGVAASGEEIATHPFQPATGCTWKGIAFGGWKSIESVPKLVSEYMSTKIKADEFMT

Parental  HNLSFDEINKAFELMHSGKSIRTVVKI
          HNLSFDEINKAFELMHSGK.IRTVVKI
Retrocopy HNLSFDEINKAFELMHSGKRIRTVVKI

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	0.00 RPM	86.94 RPM
SRP007412_kidney	0.00 RPM	192.42 RPM
SRP007412_liver	0.00 RPM	157.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_453 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_453 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_175
Pan troglodytes	retro_ptro_166
Callithrix jacchus	retro_cjac_2933

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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,