RetrogeneDB ID: retro_nleu_29

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397307.1:2608308..2609454(+)
• Located in intron of: ENSNLEG00000011582

Retrocopy information

• Ensembl ID: ENSNLEG00000018898
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSNLEG00000017780
• Aliases: None
• Description: None

Sequence

>retro_nleu_29
ATGAGTTGGACTGTGCCTATTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAATTTCCCATGCCTGGGGATGGC
CCTGTGTCCCCGTCAAGCAGGGCGCATCCCGCTCAAGGGCGCCTGGCTCTTCACCCCTGTGAGCAAGATGGCGACTGTGA
AGAGTGAGCTTATTGAGCGCTTCACTTCCGAGGAGCCCGTTCATCACAGTAAGGTCTCCATCATAGGAACTGGATCGGTG
GGCATGGCCTGTGCTATCAGCATCTTATTAAAAGGCTTGAGTGATGAACTTGCCCTTGTGGATCTTGATGAAGACAAACT
GAAGGGTGAGACAATGGATCTTCAACATGGCAGCTCTTTCACGAAAATGCCAAATATTGTTTGTAGCAAAGATTACTTTG
TCACAGCAAACTCCAACCTAGTGATTATCACAGCAGGTGCACGCCAAGAAAAGGGAGAAACACGCCTTAATTTAGTCCAG
CGAAATGTGGCCATCTTCAAGTTAATGATTTCCAGTATTGTCCAGTACAGCCCCCACTGCAAACTGATTATTGTTTCCAA
TCCAGTGGATATCTTAACTTATGTAGCTTGGAAGTTGAGTGCATTTCCCAAAAACCGTATTATTGGAAGCGGCTGTAATC
TGGATACTGCTCGTTTTCGTTTCTTGATTGGACAAAAGCTTGGTATCCATTCTGAAAGCTGCCATGGATGGATCCTCGGA
GAGCATGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATAGCTGGTGTCCCGCTGAAGGATCTGAACTCTGATAT
AGGAACTGATAAAGATCCTGAGCAATGGAAAAATGTCCACAAAGAAGTGATTGCTACTGCCTATGAGATTATTAAAATGA
AAGGTTATACTTCTTGGGCCATTGGCCTATCTGTGGCTGATTTAACAGAAAGTATTTTGAAGAATCTTAGGAGAACACAT
CCAGTTTCCACCATAATTAAGGGCCTCTATGGAATAGATGAAGAAGTATTTCTCAGTGTTCCTTGTATCCTGGGAGAAAA
TGGTATTACCAACCTTATAAAGATAAAGCTGACCCCTGAAGAAGAGGCCCATCTGAAAAAAAGTGCAAAAACACTTTGGG
AAATTCAGAAGGAGCTTAAGCTTTAA

Alignment

ORF - retro_nleu_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATVKSELTKNFAEEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDVDEGKLKGETMDLQHGSP
          MATVKSEL...F..EE..HH.K.SI.GTGSVG.ACAISILLKGLSDEL.LVD.DE.KLKGETMDLQHGS.
Retrocopy MATVKSELIERFTSEEPVHHSKVSIIGTGSVGMACAISILLKGLSDELALVDLDEDKLKGETMDLQHGSS

Parental  FMKMPNIVSSKDYLVTANSNLVIITAGARQKKGETRLDLVQRNVSIFKLMIPNITQYSPHCKLLIVTNPV
          F.KMPNIV.SKDY.VTANSNLVIITAGARQ.KGETRL.LVQRNV.IFKLMI..I.QYSPHCKL.IV.NPV
Retrocopy FTKMPNIVCSKDYFVTANSNLVIITAGARQEKGETRLNLVQRNVAIFKLMISSIVQYSPHCKLIIVSNPV

Parental  DILTYVAWKLSAFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNIAGVP
          DILTYVAWKLSAFPKNR.IGSGCNLD.ARFR..IGQ.LGIHSESCHG.ILGEHGDSSVPVWSGVNIAGVP
Retrocopy DILTYVAWKLSAFPKNRIIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP

Parental  LKDLNPDIGTDKDPEQWENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVSTLSKGL
          LKDLN.DIGTDKDPEQW.NVHK.VI...YE..KMKGYTSW.I.LSVADLTESILKNLRR.HPVST..KGL
Retrocopy LKDLNSDIGTDKDPEQWKNVHKEVIATAYEIIKMKGYTSWAIGLSVADLTESILKNLRRTHPVSTIIKGL

Parental  YGINEEIFLSVPCILGENGITDLIKVKLTLEEEACLQKSAETLWEIQKELKL
          YGI.EE.FLSVPCILGENGIT.LIK.KLT.EEEA.L.KSA.TLWEIQKELKL
Retrocopy YGIDEEVFLSVPCILGENGITNLIKIKLTPEEEAHLKKSAKTLWEIQKELKL

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_29 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 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007067	2 retrocopies	retro_cjac_164, retro_cjac_2180,
Homo sapiens	ENSG00000166800	2 retrocopies	retro_hsap_42, retro_hsap_905,
Macaca mulatta	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys	ENSNLEG00000017767	4 retrocopies	retro_nleu_1037, retro_nleu_1303, retro_nleu_1766, retro_nleu_820,
Nomascus leucogenys	ENSNLEG00000017780	2 retrocopies	retro_nleu_29 , retro_nleu_378,
Otolemur garnettii	ENSOGAG00000009261	1 retrocopy	retro_ogar_2662,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,