RetrogeneDB ID: retro_ggor_354

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:220478042..220479165(+)
• Located in intron of: ENSGGOG00000001014

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADH5
• Ensembl ID: ENSGGOG00000028244
• Aliases: None
• Description: None

Sequence

>retro_ggor_354
ATGGTGAACCAGGTTATCAAGTGCAAGGCTGCAGTTGCCTGGGAGGCTGGAAAGCCTCTCTCCGTAGAGGAGATAGAGGT
GGCACCCCCAAAGGCTCGTGAAGTTTGAATCGAGATCATTGCCACTGCAGTTTGCCACACCAATGCCTATACCCTGAGCA
GAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGGAAGTGTTGGTGAGGGAGTT
GCTAAGCTGAAGGCGGGTGATAACTGTCATCCCATTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTA
AAACTAACCTCTGCCAGAAGATAAGAGTCACTCGAGGGAAAGGATTAGTGCCAGATGGTACCAGCAGATTTACTTGCAAA
GGAAAGACAATTTTACATTACATGGGAACCAGCACATTTTCTGAATGCACAGTTGTGGCTGATATCTCTGTTGCTAAAAT
AGATTCTTTAGCACCTTTGGATAAAGTCTGCCTTCTAGGTTGTGGCATTTCAGCTGGTTATGGTGCTGCTGTGAACACTG
TCAAGGTGGGGCCTGGCTCTCTTTGTGCTGTCTTTGGCCTGGGAGGAGTTGGATTGACAGTTATCGTGGGCGGTAAAGTG
GCTGGTGCATCCCGGATCATTGGTGTGGACATCCATCAAGATAAATTTCCAAGGGCTAAAGAGTTTGGAGCCACTGAATG
TATGAACCGTCAGGATTTTAGTAAACCCATCCAGGAAGTGCTCATTGAGCTGACTGATGGAGGAGTGGACTACTCCTTTG
AATGTATTAGGAATGTCAGGGTCGTGAGAGCAGCACTTGAGGCATGTCAGCAGGGCTGGGGCGTCAGTGTGGTGGTTGGA
GTAGCTGCTTCAGGTCAAGAAATTGCCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGG
AGGGTGAAAGAGTGTAGAAAGTGTCCCAAAGTTGGTATCTGAATATGTGTCTAAAAAGATAAAAGTTGATGAATTTGTGA
CTCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTGAACTGTTGCATTCTGGAAAGAGCATTCGAACTGTTGTCAAG
ATT

Alignment

ORF - retro_ggor_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
          M.NQVIKCKAAVAWEAGKPLS.EEIEVAPPKA.EV.I.IIATAVCHT.AYTLS.ADPEGCFPVILGHEGA
Retrocopy MVNQVIKCKAAVAWEAGKPLSVEEIEVAPPKAREV*IEIIATAVCHTNAYTLSRADPEGCFPVILGHEGA

Parental  GIVESVGEGVTKLKAGD-TVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILH
          GIV.SVGEGV.KLKAGD.TVIP.YIPQCGECKFCLNPKTNLCQKIRVT.GKGL.PDGTSRFTCKGKTILH
Retrocopy GIVGSVGEGVAKLKAGD>TVIPFYIPQCGECKFCLNPKTNLCQKIRVTRGKGLVPDGTSRFTCKGKTILH

Parental  YMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVTM
          YMGTSTFSE.TVVADISVAKID.LAPLDKVCLLGCGIS.GYGAAVNT.KV.PGS.CAVFGLGGVGL.V..
Retrocopy YMGTSTFSECTVVADISVAKIDSLAPLDKVCLLGCGISAGYGAAVNTVKVGPGSLCAVFGLGGVGLTVIV

Parental  GCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAAL
          G.KVAGASRIIGVDI..DKF.RAKEFGATEC.N.QDFSKPIQEVLIE.TDGGVDYSFECI.NV.V.RAAL
Retrocopy GGKVAGASRIIGVDIHQDKFPRAKEFGATECMNRQDFSKPIQEVLIELTDGGVDYSFECIRNVRVVRAAL

Parental  EACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHN
          EAC..GWGVSVVVGVAASG.EIATRPFQLVTGRTWKGTAFGG.KSVESVPKLVSEY.SKKIKVDEFVTHN
Retrocopy EACQQGWGVSVVVGVAASGQEIATRPFQLVTGRTWKGTAFGG*KSVESVPKLVSEYVSKKIKVDEFVTHN

Parental  LSFDEINKAFELMHSGKSIRTVVKI
          LSFDEINKAFEL.HSGKSIRTVVKI
Retrocopy LSFDEINKAFELLHSGKSIRTVVKI

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	0.14 RPM	58.07 RPM
SRP007412_cerebellum	0.04 RPM	35.42 RPM
SRP007412_heart	0.00 RPM	29.93 RPM
SRP007412_kidney	0.00 RPM	167.24 RPM
SRP007412_liver	0.00 RPM	158.72 RPM
SRP007412_testis	0.00 RPM	78.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_354 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_330
Pan troglodytes	retro_ptro_266
Pongo abelii	retro_pabe_359

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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,