RetrogeneDB ID: retro_nleu_249

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:30818046..30818696(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000007146
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GLRX3
• Ensembl ID: ENSNLEG00000027088
• Aliases: None
• Description: glutaredoxin 3 [Source:HGNC Symbol;Acc:15987]

Sequence

>retro_nleu_249
ATGGTGGCGGGGGCGGCTGAGGCAGCTGTAGTGGCCCTGGAGGAGGTCAGCTCAGCCGGGTAGTTTGAGGAGCTGCTGTG
CCTCAAAGCCAAGTCCCTCCTCGTGGTCCATTTCTGGGCACCATGGGCTCCACAGTGTGCACAGATGAACGAAGTTATGG
CAGAGTTAGCTAAAGAACTCCCTCAAGTTTCATTTGTGAAGTTGGAAACTGAAGGTGTTCTGAAGTATCTGAAAAATATG
AAATTAGCTCTGTTCCCACTTTTCTGTTTTTCAAGAATTCTCAGAAAATCGACCGATTAGATGGTGCACATGCCCCAGAG
TTGACCAAAAAAGTTCAGTGACATGCATCTAGTGGCTCCTTCCCACCCCACGCTAATGAACATCTTAAAGAAGATCTCAA
CCTTCGCTTGAAGAAATTCACTCATGCTGCCCCCTGTATGCTGTTTATGAAAGGAACTCCTCAAGAACCACGCTGTGGCT
TCAGCAAGCAGATGGTGGAAATTCTTCACAAACATAATATTCAGTTTAGCAGTTTTGATATCTTCTCAGATGAAGAGGTT
CGACAGGGACTCAAAGCCTATTCCAATTGGCCTACCTATACTCAGCTCTACATTTCTGGAGAGCTCATAGGAGGACTTGA
TATAATTAAG

Alignment

ORF - retro_nleu_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.58 %
• Parental protein coverage: 84.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGAAEAAVAALEEVGSTGQFEELLRLKAKSLLVVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKLEA
          M.AGAAEAAV.ALEEV.S.G.FEELL.LKAKSLLVVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKLE.
Retrocopy MVAGAAEAAVVALEEVSSAG*FEELLCLKAKSLLVVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKLET

Parental  EGV-PEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQRHASSGSFPPSANEHLKEDLNLRLKK
          EGV..EVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQ.HASSGSFPP.ANEHLKEDLNLRLKK
Retrocopy EGV<SEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQ*HASSGSFPPHANEHLKEDLNLRLKK

Parental  LTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSNWPTYPQLYVSGEL
          .THAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSNWPTY.QLY.SGEL
Retrocopy FTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSNWPTYTQLYISGEL

Parental  IGGLDIIK
          IGGLDIIK
Retrocopy IGGLDIIK

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_249 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249 ,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,