RetrogeneDB ID: retro_nleu_895

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:32371313..32371937(-)
• Located in intron of: ENSNLEG00000016138

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A6
• Ensembl ID: ENSNLEG00000000389
• Aliases: None
• Description: None

Sequence

>retro_nleu_895
CAAGCCCTCAGCTTTGCCTTTAGGGATAAGTACGAGCGGGTCTTTCTGGGAGGCGTGCATAAGCATGCACAGTTCTGGAG
ATATTTTGCAGGCAACCTGGCTTCCTGAGGGGCGGCTGGGGCCATCTCCCTGTGCTTCTTCTACCCCCTGGAATTTGCCA
GAACCCACCTGGCAGCCAACATTGGGAAATTGGGCACATAGTGGGAGCTCAAAGGCCTGGCAGACTGCCTGGAGAAGATC
AAGGCCGATGGGATCTGAGGCCTGTCCCAGGGCTTCAGCGTCTCGGTGCAGGGCATCCATATGTACTGGGGAACCTACCT
CAGCGTGTATGATACAGCCAAGGGCATGCTCCCTGACCCCAAGAACACCCACCACATGGTGAGCTGGATGATTGCCCAGG
CCATGACAGTGGCCCATGTGGCCTCCTACCCACTCCTCACAGTGCGGGCGGATGGTGATGCAGTCCAGGTGCAAAGGAGG
TGCTATTACGAACACAGGTGCCCTTGATTGTTGGCAGAAGCTCTCCTAAGATGAAGGGGCAAAGCCTCCATCAAGGGTGC
ATGGTCCAACATCCTCACAGGCATGGGGCCAAGTCTGGGCCTGTATTATGAGCTGAAGAAAGTC

Alignment

ORF - retro_nleu_895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.44 %
• Parental protein coverage: 71.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QALNFAFKDKYKQIFLGGVDKHRQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKSSTEREF
          QAL.FAF.DKY...FLGGV.KH.QFWRYFAGNLAS.GAAGA.SLCF.YPL.FART.LAA..GK..T..E.
Retrocopy QALSFAFRDKYERVFLGGVHKHAQFWRYFAGNLAS*GAAGAISLCFFYPLEFARTHLAANIGKLGT*WEL

Parental  RGLGDCLVKITKSDGIRGLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLPDPRNTHIVVSWMIAQTVTAVA
          .GL.DCL.KI.K.DGI.GL.QGFSVSVQGI..Y...Y..VYDTAKGMLPDP.NTH..VSWMIAQ..T.VA
Retrocopy KGLADCLEKI-KADGI*GLSQGFSVSVQGIHMYWGTYLSVYDTAKGMLPDPKNTHHMVSWMIAQAMT-VA

Parental  GVVSYPFDTVR-RRMMMQSGRKGADIMYTGTVDCWRKIFRDEG-GKAFFKGAWSNVLRGMGGAFVLVLYD
          .V.SYP..TVR.R..M.QS..KG..I..TG..DCW.K...DEG.GKA..KGAWSN.L.GMG....L.LY.
Retrocopy HVASYPLLTVR>RMVM-QSRCKGGAITNTGALDCWQKLS*DEG<GKASIKGAWSNILTGMGPS--LGLYY

Parental  ELKKV
          ELKKV
Retrocopy ELKKV

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_895 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 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005609	1 retrocopy	retro_amel_255,
Homo sapiens	ENSG00000169100	5 retrocopies	retro_hsap_1207, retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla	ENSGGOG00000023004	2 retrocopies	retro_ggor_239, retro_ggor_2785,
Loxodonta africana	ENSLAFG00000001584	1 retrocopy	retro_lafr_713,
Microcebus murinus	ENSMICG00000006136	2 retrocopies	retro_mmur_1021, retro_mmur_922,
Macaca mulatta	ENSMMUG00000006899	1 retrocopy	retro_mmul_1182,
Nomascus leucogenys	ENSNLEG00000000389	1 retrocopy	retro_nleu_895 ,
Nomascus leucogenys	ENSNLEG00000014852	7 retrocopies	retro_nleu_131, retro_nleu_1314, retro_nleu_1383, retro_nleu_1679, retro_nleu_2253, retro_nleu_2560, retro_nleu_3105,
Otolemur garnettii	ENSOGAG00000000963	2 retrocopies	retro_ogar_2492, retro_ogar_2499,