RetrogeneDB ID: retro_nleu_1772

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397308.1:9652312..9653435(+)
• Located in intron of: ENSNLEG00000003621

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADH5
• Ensembl ID: ENSNLEG00000013946
• Aliases: None
• Description: None

Sequence

>retro_nleu_1772
ATGGCGAACCAGGTTATCAAGTGCAAGGCTGCAGTTGCCTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCACCCCCAAAGGCTCATGAAGTTTGAATCAAGATCATTGCCACTGCAGTTTGCCACACCGATGCCTGTACCCTGAGCG
GAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGGAAGTGTTGGTGAGGGAGTT
ACTAAGCTGAAGGCGGGTGATAACTGTCATCCCATTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTA
AAACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAATGCCAGATGGTACCAGCAGATTTACTTGCAAA
GGAAAGACAATTTTACATTACATGGGAACCAGCACATTTTCTGGATGCACAGTTGTGGCTGATATCTCTGTTACTAAAAT
AGATTCTTTAGCACCTTTGGATAAAGTCTGCCTTTTAGGTTGTGGCATTTCAACTGGTTATGGTGCTGCTGTGAACACTG
TCAAGGTGGAGCCTGGCTCTGTTTGTGCCATCTTTGGCCTGGGAGGAGTTGGATTGACAGTTATCGTGGGCGGTAAAGTG
TCTGGTGCATCCTGGATCATTGGTGTGGACATCAATCAAGATAAATTTCTAAGGGCTAAAGAGTTTGGAGCCACTGAATG
TATGAGCCCTCAGGATTTTAATAAACCCATCCAGGAAGTGCTCATTGAGATGACTGATGGAGGAGTGGACTACTCCTTTG
AATGTATTAGGAATGTCAAGGTCGTGAGAGCAGCATTTGAGGCATGTCAGCAGGGCTGGGGCATCAACGTGGTGGTTGGA
GTAGCTGCTTCAGGTCAAGAAATTGCCACTCGTCTATTCCAGCTGGTAACATGTCGCACATGGAAAGGCAGTGCCTTTGG
AGGGTGAAAGAGTGTAGGAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAGATAAAAGTTGATGAATTTGCAA
CTCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTCAACTGATGCATTCTGGAAAGAGCATTCGAACTGTTGTCAAG
ATT

Alignment

ORF - retro_nleu_1772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
          MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEV.IKIIATAVCHTDA.TLSGADPEGCFPVILGHEGA
Retrocopy MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEV*IKIIATAVCHTDACTLSGADPEGCFPVILGHEGA

Parental  GVVESVGEGVTKLKAGD-TVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILH
          G.V.SVGEGVTKLKAGD.TVIP.YIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILH
Retrocopy GIVGSVGEGVTKLKAGD>TVIPFYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILH

Parental  YMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIM
          YMGTSTFS..TVVADISV.KID.LAPLDKVCLLGCGISTGYGAAVNT.KVEPGSVCA.FGLGGVGL.VI.
Retrocopy YMGTSTFSGCTVVADISVTKIDSLAPLDKVCLLGCGISTGYGAAVNTVKVEPGSVCAIFGLGGVGLTVIV

Parental  GCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAAL
          G.KV.GAS.IIGVDIN.DKF.RAKEFGATEC..PQDF.KPIQEVLIEMTDGGVDYSFECI.NVKV.RAA.
Retrocopy GGKVSGASWIIGVDINQDKFLRAKEFGATECMSPQDFNKPIQEVLIEMTDGGVDYSFECIRNVKVVRAAF

Parental  EACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHN
          EAC..GWG..VVVGVAASG.EIATR.FQLVT.RTWKG.AFGG.KSV.SVPKLVSEYMSKKIKVDEF.THN
Retrocopy EACQQGWGINVVVGVAASGQEIATRLFQLVTCRTWKGSAFGG*KSVGSVPKLVSEYMSKKIKVDEFATHN

Parental  LSFDEINKAFELMHSGKSIRTVVKI
          LSFDEINKAF.LMHSGKSIRTVVKI
Retrocopy LSFDEINKAFQLMHSGKSIRTVVKI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1772 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,