RetrogeneDB ID: retro_nleu_1856

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397313.1:8175170..8175492(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSNLEG00000007299
• Aliases: None
• Description: 6-pyruvoyl tetrahydrobiopterin synthase [Source:UniProtKB/TrEMBL;Acc:G1R6T3]

Sequence

>retro_nleu_1856
AGCCACAGGCTGGCACAGCAAATCTCTGAGTATCAAAGAAACCATCAAACAGTTTTAGAACTGCAGCAATGCAAATGTCC
ATGAACATGATTATAAAGTTATAGTTATAGTATATGGAGGGATTGATCCAGTTACAGGAATGGTTATGAATACGATCAAC
CTCACAAAGTATATGGAGGAGGCAATTATGAAGCCCCTTGATCATAAGAATCTGGACCTGGATGTACCATACTTTGCAGA
TGTTCTAAGCATGAAAGAAAAGGTAGTTGGATATATCTGGTGAAACATCCAGAAATTTCTTCCTGTAGAAGTTATTTATA
AA

Alignment

ORF - retro_nleu_1856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 73.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHRL-YSKFLSDEENLKLFGKCSNPNGHGHNYKVVVTVHGEIDPATGMVMNLADLKKYMEEAIMEPLDHK
          SHRL..SK.LS..E..K.F..CSN.N.H.H.YKV.V.V.G.IDP.TGMVMN...L.KYMEEAIM.PLDHK
Retrocopy SHRL>HSKSLSIKETIKQF*NCSNANVHEHDYKVIVIVYGGIDPVTGMVMNTINLTKYMEEAIMKPLDHK

Parental  NLDMDVPYFADVVSTTENVAVYIWDNLQKVLPVGVLYK
          NLD.DVPYFADV.S..E.V..YIW.N.QK.LPV.V.YK
Retrocopy NLDLDVPYFADVLSMKEKVVGYIW*NIQKFLPVEVIYK

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_1856 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925, retro_chof_2556,
Callithrix jacchus	ENSCJAG00000012437	2 retrocopies	retro_cjac_2534, retro_cjac_2853,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Homo sapiens	ENSG00000150787	1 retrocopy	retro_hsap_3408,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Nomascus leucogenys	ENSNLEG00000007299	1 retrocopy	retro_nleu_1856 ,
Otolemur garnettii	ENSOGAG00000017191	3 retrocopies	retro_ogar_1718, retro_ogar_2790, retro_ogar_609,
Pongo abelii	ENSPPYG00000003880	1 retrocopy	retro_pabe_432,
Pan troglodytes	ENSPTRG00000004288	3 retrocopies	retro_ptro_2315, retro_ptro_2979, retro_ptro_337,