RetrogeneDB ID: retro_nleu_2048

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397324.1:8654341..8654861(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD2
• Ensembl ID: ENSNLEG00000017430
• Aliases: None
• Description: None

Sequence

>retro_nleu_2048
ACTGGGTCAAAGAGTAGGCCGAGCACACTCAACTGGAAGAATAGCAAACAGGAAGTCATCATGGCCCCAATGTCTACTCA
TGGAAACCAAGAGAAAGGTCCCCATTGGCCACGACCAAGCAAGCAGAGCCTGTTGTTTTATCCAAAATCAAACTGCACAT
CCACAGAGGAGAGATTTCAAACATTGTAAGAGGATGTCAAGAAGAAAGTTTCTGGAAGAGAGCTCCGCCTTTTTCTCCTG
TAAGCGTGCTTGTCACCCAGGGACTAGTCTGCCAAGGTTATTTAGCAGCTAATCCAAGATTTGGATCATTGCCTAAAGTT
ACACTTGTTGGTATCTTGGGATTGGCCTTGGAAAGGTATCATACATAAGAGTATGCCACAGTAAATTCCATTTCTTTGAA
GATCAGCTCCATGGGGCTGATTTTGGTCCACAGCAGAACAGGCATTGATTGCTTACCTGTGAAGAATGCAAAATAAAGAA
TGGATTCAATGAGAAGGGAAGTTCACAGCCTTTGGCTTCC

Alignment

ORF - retro_nleu_2048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 78.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGSRSKQRINDWKESKHKVIMASASARGNQDKDPHFPPPSKQSLLFCPKS-KLHIHRAEISKIMRECQEE
          TGS.S......WK.SK..VIMA..S..GNQ.K.PH.P.PSKQSLLF.PKS.KLHIHR.EIS.I.R.CQEE
Retrocopy TGSKSRPSTLNWKNSKQEVIMAPMSTHGNQEKGPHWPRPSKQSLLFYPKS<KLHIHRGEISNIVRGCQEE

Parental  SFWKRALPFSLVSMLVTQGLVYQGYLAANPRFGSLPKVALAGL-LGFGLGKVSYIGVCQSKFHFFEDQLR
          SFWKRA.PFS.VS.LVTQGLV.QGYLAANPRFGSLPKV.L.G..LG.GLGKVSYI.VC.SKFHFFEDQL.
Retrocopy SFWKRAPPFSPVSVLVTQGLVCQGYLAANPRFGSLPKVTLVGI<LGIGLGKVSYIRVCHSKFHFFEDQLH

Parental  GAGFGPQHNRHCLLTCEECKIKHGLSEKGDSQPSAS
          GA.FGPQ.NRH.LLTCEECKIK.G..EKG.SQP.AS
Retrocopy GADFGPQQNRH*LLTCEECKIKNGFNEKGSSQPLAS

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_2048 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018637	1 retrocopy	retro_cjac_1505,
Erinaceus europaeus	ENSEEUG00000006759	1 retrocopy	retro_eeur_504,
Homo sapiens	ENSG00000145247	1 retrocopy	retro_hsap_4082,
Gorilla gorilla	ENSGGOG00000013778	1 retrocopy	retro_ggor_2738,
Microcebus murinus	ENSMICG00000006147	1 retrocopy	retro_mmur_1402,
Macaca mulatta	ENSMMUG00000014869	1 retrocopy	retro_mmul_2353,
Monodelphis domestica	ENSMODG00000025531	1 retrocopy	retro_mdom_1006,
Nomascus leucogenys	ENSNLEG00000017430	1 retrocopy	retro_nleu_2048 ,
Oryctolagus cuniculus	ENSOCUG00000007907	2 retrocopies	retro_ocun_1734, retro_ocun_1780,
Otolemur garnettii	ENSOGAG00000011039	1 retrocopy	retro_ogar_561,
Pongo abelii	ENSPPYG00000014722	1 retrocopy	retro_pabe_3350,
Pan troglodytes	ENSPTRG00000016048	1 retrocopy	retro_ptro_2768,
Vicugna pacos	ENSVPAG00000011765	1 retrocopy	retro_vpac_331,