RetrogeneDB ID: retro_nleu_2636

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397384.1:4257367..4258468(-)
• Located in intron of: None

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_2636
ATGGCGAACCAGGTTATCAAGTGCAAGGCTGCAGCTGCTTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCACCCCCAAAGGCTCATGAAGTTCGAATCAAGATCATTGCCACTGCGGTTTGCCACACCAAGGCCTATATCCTGAGCG
GAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGTACATGAAGGTGCTGGAATTGTGGAAAGCGTTGGTGAGGGAGTT
ACTAAGCTGAAGGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTAA
AACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAACGATTAATGTCAGATGGTACCAGCAGATTTACTTGCAAAG
GAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTTGGCTGATATCTCTGTTGCTAAAATAG
ATCCTTTAGCACTTTTGGATAAAGTCTGCCTTCTAGGTTGTGGCATTTCAACTGGCAATGGTGCTGCTGTGAACACTGCC
AAGGTGGAGCCTGGCTCTGTTTGTGCCATCTTTGGTCTGGGAGGAGTTGGATTGGCAGTTATCATGGGCTGTAAAGTGGC
TGGTGCATCCCGGATCATTGATGTGGACATCAATAAAGATAAATTTGCAAGGACCAAAGCGTTTGGAGCCACTGAATGTA
GTAAACCCATCCAGGAAGTGCTCATTGAGATGACTGATGGAGAAGTGGACTATTCCTTTCAATGTATTGGTAATGTGAAG
GTCATGAGAGCAGCACTTGAGGCGTGTCACAAGGGCTGGGGCGTCAGTGTGGTGGTTGGAGTAGCTGCTTCAGGTGAAGA
AATTGTCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGACACTGCCTTTGGAGGATGGAAGAGTGTACAGT
GTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAGATAAACGTTGATTAATTTGTGACTCACAATCTGTCTTTTGATGA
AATTAACAAAGCCTTTGAACTGATGCATTCTGGAAAGAGCATTCGAACTGTTGTAAAGATT

Alignment

ORF - retro_nleu_2636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
          MANQVIKCKAA.AWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHT.AY.LSGADPEGCFPVIL.HEGA
Retrocopy MANQVIKCKAAAAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTKAYILSGADPEGCFPVILVHEGA

Parental  GVVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHY
          G.VESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGK.LM.DGTSRFTCKGKTILHY
Retrocopy GIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKRLMSDGTSRFTCKGKTILHY

Parental  MGTSTFSEYTV-VADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIM
          MGTSTFSEYTV..ADISVAKIDPLA.LDKVCLLGCGISTG.GAAVNTAKVEPGSVCA.FGLGGVGLAVIM
Retrocopy MGTSTFSEYTV<LADISVAKIDPLALLDKVCLLGCGISTGNGAAVNTAKVEPGSVCAIFGLGGVGLAVIM

Parental  GCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAAL
          GCKVAGASRI...D....K......F..T........SKPIQEVLIEMTDG.VDYSF.CIGNVKVMRAAL
Retrocopy GCKVAGASRI--IDVDINK----DKFARTKAFGATECSKPIQEVLIEMTDGEVDYSFQCIGNVKVMRAAL

Parental  EACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPK-LVSEYMSKKIKVDEFVTH
          EACHKGWGVSVVVGVAASGEEI.TRPFQLVTGRTWK.TAFGGWKSV...PK.LVSEYMSKKI.VD.FVTH
Retrocopy EACHKGWGVSVVVGVAASGEEIVTRPFQLVTGRTWKDTAFGGWKSVQ-CPK>LVSEYMSKKINVD*FVTH

Parental  NLSFDEINKAFELMHSGKSIRTVVKI
          NLSFDEINKAFELMHSGKSIRTVVKI
Retrocopy NLSFDEINKAFELMHSGKSIRTVVKI

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_2636 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,