RetrogeneDB ID: retro_nleu_22

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397291.1:19434442..19435549(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018370
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ENSG00000111275
• Ensembl ID: ENSNLEG00000000016
• Aliases: None
• Description: None

Sequence

>retro_nleu_22
TTTGCTGGCTGGGCTGACAAGTGGCATGGCAAGACCATCCCCATGGATGGCCCAGCATTCTGCTTCACCCGGCATGAGCC
CGTTGGTGTCTGTGGCCAGATCATCCCGTGGAACTTCCCTTTGGTCATGCAGGGTTGGAAACTTGCCCCCGCACTCGCCA
CAGGCAACACTGTGGTTATGAAGGTGGCAGAGCAGACCCCCCTCTCTGCCCTGTATTTGGCTTCCCTCATCAAGGAGGCA
GGCTTTCCCCCTGGGGTCGTGAACATCATCACGGGCTATGGCCCAACTGCAGGTGCGGCCATCGCACAGCACATGGATGT
TGACAAAGTTGCCTTCACCGGTTCCACCGAGGTGGGCCACCTGATCCAGAAAGCAGCTGGCGATTCCAACCTCAAGAGAG
TCACTCTGGAGCTGGGTGGTAAGAGCCCCAGCATTGTGCTGGCCGATGCTGACATGGAGCATGCCGTGGAGCAGTGTCAC
GAAGCCCTGTTCTTCAACATGGGCCAGTGCTGCTGTGCTGGCTCCCGGACCTTCGTGGAAGAATCCATCTACAATGAGTT
TCTCGAGAGAACCGTGGAGAAAGCAAAGCAGAGGAAAGTGGGGAACCCCTTTGAGCTGGACACACAGCAGGGGCCTCAGG
TGGACAAAGAGCAGTTTGAACGAGTCCTAGGCTACATCCAGCTTGGCCAGAAGGAGGGCGCAAAACTCCTCTGTGGCGGA
GAGCGTTTTGGGGAGCGTGGTTTCTTCATCAAGCCTACTGTCTTTGGTGGCGTGCAGGATGACATGAGAATTGCCAAAGA
GGAGATCTTTGGGCCTGTGCAGCCCCTGTTCAAGTTCAAGAAGATTGAAGAGGTGATTGAGAGGGCCAACAACACCAGAT
ATGGCCTGGCTGCGGCTGTGTTCACCCGGGATCTGGACAAAGCCATGTACTTCACCCAGGCACTCCAGGCCGGGACCGTG
TGGGTAAACACCTACAACATCGTCACCTGCCACACACCATTTGGAGGGTTTAAGGAATCTGGAAATGGGAGGGAGCTGGG
TGAGGATGGGCTTAAGGCCTACACAGAGGTGAAGACGGTCACCATCAAGGTTCCTCAGAAGAACTCG

Alignment

ORF - retro_nleu_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.98 %
• Parental protein coverage: 77.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA
          .AGWADK.HGKTIP.DG..F..TRHEPVGVCGQIIPWNFPL.MQ.WKL.PALATGN.VVMKVAEQTPL.A
Retrocopy FAGWADKWHGKTIPMDGPAFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKVAEQTPLSA

Parental  LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGG
          LY.A.LIKEAGFPPGVVNI..G.GPTAGAAIA.H.DVDKVAFTGSTE.G..IQ.AAG.SNLKRVTLELGG
Retrocopy LYLASLIKEAGFPPGVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGG

Parental  KSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSKTEQ
          KSP.I...DADM..AVEQ.H.ALFFN.GQCCCAGSRTFV.E.IY.EF.ER.V..AK.R.VGNPF...T.Q
Retrocopy KSPSIVLADADMEHAVEQCHEALFFNMGQCCCAGSRTFVEESIYNEFLERTVEKAKQRKVGNPFELDTQQ

Parental  GPQVDETQFKKILGCINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDV-DGMTIAKEEIFGPVMQILKFK
          GPQVD..QF...LG.I..G..EGAKLLCGG.....RG.FI.PTVFG.V.D.M.IAKEEIFGPV....KFK
Retrocopy GPQVDKEQFERVLGYIQLGQKEGAKLLCGGERFGERGFFIKPTVFGGVQDDMRIAKEEIFGPVQPLFKFK

Parental  TIEEVVGRANNSTYGLAAAVFAKDLDKANYLSQALQVGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYG
          .IEEV..RANN..YGLAAAVF..DLDKA.Y..QALQ.GTVWVN.Y.......PFGG.K.SG.GRELGE.G
Retrocopy KIEEVIERANNTRYGLAAAVFTRDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRELGEDG

Parental  LQAYTEVKTVTVKVPQKNS
          L.AYTEVKTVT.KVPQKNS
Retrocopy LKAYTEVKTVTIKVPQKNS

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_22 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 21 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013664	1 retrocopy	retro_amel_51,
Bos taurus	ENSBTAG00000008743	1 retrocopy	retro_btau_48,
Canis familiaris	ENSCAFG00000008683	1 retrocopy	retro_cfam_1493,
Equus caballus	ENSECAG00000017673	2 retrocopies	retro_ecab_1054, retro_ecab_1061,
Felis catus	ENSFCAG00000022000	1 retrocopy	retro_fcat_1590,
Homo sapiens	ENSG00000111275	1 retrocopy	retro_hsap_19,
Gorilla gorilla	ENSGGOG00000007108	1 retrocopy	retro_ggor_33,
Latimeria chalumnae	ENSLACG00000011798	1 retrocopy	retro_lcha_108,
Microcebus murinus	ENSMICG00000003487	1 retrocopy	retro_mmur_19,
Myotis lucifugus	ENSMLUG00000017084	1 retrocopy	retro_mluc_1918,
Macaca mulatta	ENSMMUG00000008336	1 retrocopy	retro_mmul_247,
Mustela putorius furo	ENSMPUG00000002282	1 retrocopy	retro_mputfur_27,
Mus musculus	ENSMUSG00000029455	1 retrocopy	retro_mmus_222,
Nomascus leucogenys	ENSNLEG00000000016	1 retrocopy	retro_nleu_22 ,
Otolemur garnettii	ENSOGAG00000033093	1 retrocopy	retro_ogar_203,
Pongo abelii	ENSPPYG00000004966	1 retrocopy	retro_pabe_32,
Pteropus vampyrus	ENSPVAG00000013189	1 retrocopy	retro_pvam_163,
Rattus norvegicus	ENSRNOG00000001344	1 retrocopy	retro_rnor_307,
Sus scrofa	ENSSSCG00000009889	1 retrocopy	retro_sscr_9,
Ictidomys tridecemlineatus	ENSSTOG00000015009	1 retrocopy	retro_itri_33,
Xenopus tropicalis	ENSXETG00000020930	1 retrocopy	retro_xtro_12,