RetrogeneDB ID: retro_nleu_2251

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397338.1:5753539..5754053(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAR1
• Ensembl ID: ENSNLEG00000016578
• Aliases: None
• Description: None

Sequence

>retro_nleu_2251
ATGTCTTTTCAGGGCGGAGGTCGTGGAGGCTTTGATCGAGGTGGTGGAGGTGGCGGTTTCAACCACGGCAGCAGCAGCAA
CCACATCTGAGGTGGAGGCAGTGGAAGTATCAGGGGTGGCGATGGGAGGATTTGGACGAGGGGGTGGCCACAGAGGCTTT
AACAAAGGCCAAGGCCAAGGACCTCCAGAACGTGTAGTCTTATTAGGAGAGTTCCGGCATCCCTGTGAAGATGACATAGT
TTGTAAACGTACTACAGATGAAAATAAGGGGCCTTATTTCAATGCTCCTATTTACTTAGAAAACAAAGAACAAATTGGAA
AAGCGGATGAAATATTTGGACAACTTAGAGATTTTTATTTTTCCGTTAAAATGTCAGAAAACGGGAAGGCTTCATCCTTT
AAAAAACTCTAGAAGTTTTATATAGACCCATATAAGCTGCTGCCACGGCAGAGGTTTTTACCTCGACCTTCGGGTGAGAA
AGGACCTCCAAGATGTGGTGGCAGGGGAGGCCGA

Alignment

ORF - retro_nleu_2251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 81.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFRGGGRGGFNRGAGGGGFNRGGSSNHFRGGGGGG-GGGNFRGGARGGFGRGGGRGGFNKGQDQGPPER
          MSF.GGGRGGF.RG.GGGGFN.G.SSNH..GGG.G...G....G..RGG..RG...G....GQ..GPPER
Retrocopy MSFQGGGRGGFDRGGGGGGFNHGSSSNHI*GGGSGS>SGVAMGGFGRGGGHRGFNKG---QGQ--GPPER

Parental  VVLLGEFLHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFK
          VVLLGEF.HPCEDDIVCK.TTDENK.PYFNAP.YLENKEQIGK.DEIFGQLRDFYFSVK.SEN.KASSFK
Retrocopy VVLLGEFRHPCEDDIVCKRTTDENKGPYFNAPIYLENKEQIGKADEIFGQLRDFYFSVKMSENGKASSFK

Parental  KLQKFYIDPYKLLPLQRFLPRPPGEKGPPRGGGRGGR
          KL.KFYIDPYKLLP.QRFLPRP.GEKGPPR.GGRGGR
Retrocopy KL*KFYIDPYKLLPRQRFLPRPSGEKGPPRCGGRGGR

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_2251 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251 ,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,