RetrogeneDB ID: retro_nleu_343

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:10344817..10345126(-)
• Located in intron of: ENSNLEG00000004259

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSNLEG00000003257
• Aliases: None
• Description: None

Sequence

>retro_nleu_343
AGGACACTTGAGCAGGAGATTGAACATCTTAGTGAATAGTGTTCCTGGCAGCTGGAGGAACAGCAGATGATGATCCAGGA
GCAGATGTGCCAGGAACTTGATTTGAGATTAAAAGTCAGAAAATACTGAAGACAAAGGAACCCAAAACTAAAACTGAAAT
GAAAGTGCAAGAAGGATGAGTCAGAAGGCAGTTACTCCAGAGGTGTCCTCTTGTGGCTTTTGCAAAAGTATGGTGGAATT
CTCAACTTGGTGCTTTTGAGTAAGAAGGCAGGTACTGGTGTTGTGGAGTTTGGGACTGTTGATGCTGCA

Alignment

ORF - retro_nleu_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.21 %
• Parental protein coverage: 51.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTLFLEIERLREEGSRQLEEQQRLIREQIRQERDQRLRGKAENTEGQGTPKLKLKWKCKKEDESKGGYSK
          .TL..EIE.L.E..S.QLEEQQ..I.EQ..QE.D.RL..K......Q..PKLKLK.KCKK.DES.G.YS.
Retrocopy RTLEQEIEHLSE*CSWQLEEQQMMIQEQMCQELDLRL--KVRKY*RQRNPKLKLK*KCKK-DESEGSYSR

Parental  DVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAA
          .VLL.LLQKYG..LNLVL.SKK.GT.VVEF.TV.AA
Retrocopy GVLLWLLQKYGGILNLVLLSKKAGTGVVEFGTVDAA

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_343 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343 ,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,