RetrogeneDB ID: retro_nleu_1140

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:20975449..20975816(-)
• Located in intron of: ENSNLEG00000012888

Retrocopy information

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

Parental gene information

• Parental gene symbol: GATC
• Ensembl ID: ENSNLEG00000015651
• Aliases: None
• Description: Glutamyl-tRNA(Gln) amidotransferase subunit C, mitochondrial [Source:UniProtKB/TrEMBL;Acc:G1S0F5]

Sequence

>retro_nleu_1140
CTGGGTGGGCGCCAGAGCTTCACCTCCGAGGCGGATCCTCAGGGCAGTGGCCAGATCATGACTGAGGTGCTTGAGCCCCT
GGAGCCTCTAGTGCCTGTGGACTTTGGCAGTCGCAAGGCAGTGGTGCGGCTGGAGAAAGCCATCATCTTCACCCATGGGC
TCCACCCCATGGACACCGACGGGTGGAGCCCATGGAGTCGGGCCTGGAGGGCAGACGTCTATACCTGAGATCCGACAATG
TAGTAGAAGGCAACTGTGCTGAAGAATTACTACAAAATTCCCATTGCGTCGTGAAGGAGTATTTTGTGGCTCCCCAGGTA
ATATCTCTTTGCCAAAGCTGGATGAACAATAGCCTTTCTCACATAGC

Alignment

ORF - retro_nleu_1140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.4 %
• Parental protein coverage: 90.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGGRQGFTSKADLQGSGRITAELIEHLERLALVDFGSREAVARLEKAIAFADRLRAVDTDG-VEPMESVL
          LGGRQ.FTS.AD.QGSG.I..E..E.LE.L..VDFGSR.AV.RLEKAI.F...L...DTDG.VEPMES.L
Retrocopy LGGRQSFTSEADPQGSGQIMTEVLEPLEPLVPVDFGSRKAVVRLEKAIIFTHGLHPMDTDG<VEPMESGL

Parental  EDRCLYLRSDNVVEGNCADELLQNSHRVMEEYFVAP-PGNISLPKLDEQEPFPHS
          E.R.LYLRSDNVVEGNCA.ELLQNSH.V..EYFVAP.PGNISLPKLDEQ.PF.HS
Retrocopy EGRRLYLRSDNVVEGNCAEELLQNSHCVVKEYFVAP<PGNISLPKLDEQ*PFSHS

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_1140 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013298	1 retrocopy	retro_amel_1364,
Equus caballus	ENSECAG00000011118	1 retrocopy	retro_ecab_462,
Felis catus	ENSFCAG00000024015	1 retrocopy	retro_fcat_1279,
Homo sapiens	ENSG00000257218	1 retrocopy	retro_hsap_3902,
Nomascus leucogenys	ENSNLEG00000015651	1 retrocopy	retro_nleu_1140 ,
Oryctolagus cuniculus	ENSOCUG00000009867	2 retrocopies	retro_ocun_585, retro_ocun_858,
Ochotona princeps	ENSOPRG00000004226	1 retrocopy	retro_opri_1008,
Pongo abelii	ENSPPYG00000005030	1 retrocopy	retro_pabe_3181,
Pan troglodytes	ENSPTRG00000005534	1 retrocopy	retro_ptro_2655,
Sus scrofa	ENSSSCG00000009907	1 retrocopy	retro_sscr_746,
Tursiops truncatus	ENSTTRG00000000144	1 retrocopy	retro_ttru_1695,