RetrogeneDB ID: retro_ptro_2438

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:66084089..66085210(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000018324
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ADH5
• Ensembl ID: ENSPTRG00000016303
• Aliases: None
• Description: None

Sequence

>retro_ptro_2438
ATGGCGAACCAGGTTATGAAGTGCAAGGCTGCAGTTGCTTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCACCCCCAAAGGCTCATGAAGTTCGAATCAAGATCATTGCCACTGCGGTTTGCCACACCGACGCCTGTACCCTGAGGG
GAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGAGGAAAGTGTTGGCGAGGGAGTT
ACTAAGCTGAAGGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTATGGAGAATGCGAATTTTGTCTAAATCCTAA
AACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGATTTAATGCCAGATGGTACCAGCAGATTTACTTGCAAAG
GAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTAGCTGATATCTCTGTTGCTAAAATA
GATCCTTTAGCACCTTTGGATAAACTCTGCCTTCTAGGTTGTGGCATTTCAGCTGGTGATGGTGCTGCTGTGAACACTGC
CAAGGTGGAGCCTGGCTCTGTTTGTGCCGTCTTTGGTCTGGGAGGAGTTGGATTGGCAGTTATCAAGGGCTGTAAAGTGG
CTGGTGCATCCCGGACCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCCAAAGAGTTTGGAGCCACTGAATGT
ATTAACCCTCAGGGTTTTAGTAAACCCATCCAGGAAGGGCTCATTGAAATGACTGATGGAGGAGTGGACTATTCCTTTGA
ATGTATTGGTAATGTGAAGGTCATGAGAGCAGCACTTGAGGCTTATCACAAGGGCTGGGGAATCAGCGTGGTGGTTGGAG
TAGCTGCTTCAGGTGAAGAAATTGCCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGAACTGCCTTTGGA
GGATGGAAGAGTGTAGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAATAAAAGTTGATGAATTTGTGACT
CACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTCAACTGATGCATTCTGGAAAGAGCATTCGAACTGTTGTAAAGAT
T

Alignment

ORF - retro_ptro_2438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANEVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
          MAN.V.KCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDA.TL.GADPEGCFPVILGHEGA
Retrocopy MANQVMKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDACTLRGADPEGCFPVILGHEGA

Parental  GIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHY
          GI.ESVGEGVTKLKAGDTVIPLYIPQ.GEC.FCLNPKTNLCQKIRVTQGK.LMPDGTSRFTCKGKTILHY
Retrocopy GIEESVGEGVTKLKAGDTVIPLYIPQYGECEFCLNPKTNLCQKIRVTQGKDLMPDGTSRFTCKGKTILHY

Parental  MGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIMG
          MGTSTFSEYTVVADISVAKIDPLAPLDK.CLLGCGIS.G.GAAVNTAKVEPGSVCAVFGLGGVGLAVI.G
Retrocopy MGTSTFSEYTVVADISVAKIDPLAPLDKLCLLGCGISAGDGAAVNTAKVEPGSVCAVFGLGGVGLAVIKG

Parental  CKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAALE
          CKVAGASR.IGVDINKDKFARAKEFGATECINPQ.FSKPIQE.LIEMTDGGVDYSFECIGNVKVMRAALE
Retrocopy CKVAGASRTIGVDINKDKFARAKEFGATECINPQGFSKPIQEGLIEMTDGGVDYSFECIGNVKVMRAALE

Parental  ACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKK-IKVDEFVTHS
          A.HKGWG.SVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKK.IKVDEFVTH.
Retrocopy AYHKGWGISVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKK<IKVDEFVTHN

Parental  LSFDEINKAFELMHSGKSIRTVVKI
          LSFDEINKAF.LMHSGKSIRTVVKI
Retrocopy LSFDEINKAFQLMHSGKSIRTVVKI

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	0.04 RPM	26.79 RPM
SRP007412_cerebellum	0.00 RPM	30.29 RPM
SRP007412_heart	0.03 RPM	114.66 RPM
SRP007412_kidney	0.10 RPM	187.46 RPM
SRP007412_liver	0.20 RPM	169.86 RPM
SRP007412_testis	0.00 RPM	42.47 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2438 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2438 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3607
Gorilla gorilla	retro_ggor_2434
Pongo abelii	retro_pabe_176

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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,