RetrogeneDB ID: retro_nleu_1054

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397279.1:21425696..21426216(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000172062
• Ensembl ID: ENSNLEG00000004454
• Aliases: None
• Description: None

Sequence

>retro_nleu_1054
ATGGCAACGGGCAGTGCCAGCAGTGGCTGTGGCATCCTGAGCAGGAAGATTTGGTGCAGTTCTAGTGCAGCATAGGCCAG
AGTGATGATTCTGACATTTGGGATGCTACAGCACTGATAAAAGTGGATGATAAAGCTGTGGCTTCATTTAAACAGGCTCT
AAAGAATGATGACATTTGTGAAACTTCAGATAAACCAAAAAGCATGCCTAACAGAAAACCTGCTAAGAAGAATAAAAGCC
AGAAAAAGAATACTGCAACTTTCTTGAAGTGGTGGAAAGTTGGGGATAGATGTTCTGCCATTTGGTCAGAAGACAGCTGC
ATTTACTCTGCTACCATTGCTTCAGTTGATATGAAGAGAGAAAGCTGTGTTGTGATTTACACTGGATATGGAAATAGAGA
GGAGCAAATCTGTCTGATCTACTTTCTTCGACCTCTGTAGCTAATAATATAGGACAGAATGCTCAAGAGAATGAAAATGA
AAGTCAAGATTCAATGGGTGAAAGTGAGAACTCCAGATCC

Alignment

ORF - retro_nleu_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.71 %
• Parental protein coverage: 59.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAMSSGGNGGGV-PEQEDSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTT
          MA..S...G.G..PEQED.V.F....GQSDDSDIWD.TALIK..DKAVASFK.ALKN.DICETS.KPK..
Retrocopy MATGSASSGCGI<PEQEDLVQF*CSIGQSDDSDIWDATALIKVDDKAVASFKQALKNDDICETSDKPKSM

Parental  PKRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWSEDGCIYPATIVSIDFKRETCVVVYTGYGNREEQ-NL
          P.RKPAKKNKSQKKNTA..L..WKVGD.CSAIWSED.CIY.ATI.S.D.KRE.CVV.YTGYGNREEQ.NL
Retrocopy PNRKPAKKNKSQKKNTATFLKWWKVGDRCSAIWSEDSCIYSATIASVDMKRESCVVIYTGYGNREEQ<NL

Parental  SDLLSPISEVANNIEQNAQENENESQVSTDESENSRS
          SDLLS..S.VANNI.QNAQENENESQ.S..ESENSRS
Retrocopy SDLLSSTS-VANNIGQNAQENENESQDSMGESENSRS

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_1054 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054 ,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,