RetrogeneDB ID: retro_nleu_1976

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397320.1:4472535..4473357(-)
• Located in intron of: ENSNLEG00000003055

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSNLEG00000012362
• Aliases: None
• Description: None

Sequence

>retro_nleu_1976
GCGCCCTCCAGGAGTCTTGCAGTTCCCCTGCAGTCCTGGTACTGTTGCTTTGGGGTGCTCCCTGGACCCACAGGTGGCAG
AGCAACATACGCATTATCACAGACAAGAACTGGAGAAAGCTGCTGGAAGGAGACTGGATGATAGAATTTTATGCCCCGTG
GTGCCCTGCTTGTCAAAACCTTCAACTGGAATGGGAAAGTTTTGCTGAATGGGGAGAAGATCTGAGGTTAATGTTGTGAA
AGTAGATGTCACAGAGCAGCCAGGACTGACTGGACAGTTTACAATAACTGCTCTTCCTACTATTTATCATTGTAAAGATG
GTGAATTTAGGCATCCTCAGGGTCCAAGGACCAAGAAGGACTTCATAAACTTTATAAGTGATAAAGAGTGGAAGAGTATT
GAACCTGTTTCATCATGGTTTGGTCCAGGTTCTGTTCAGATGAGTAGTATGTCAGCACTCTTTCAGCTATCTCTGTGGAT
CAGGACTTGCCATAACTACTTTATTGAAGACCTTGAATTGCCAGTGTGGGGATCATACACTGTTTTTCCTTTAGCAACTC
TGCACTCTGGACTGTTACTAGGACTCTGTATGATATTTGCGGCAGATTGCCTTTGTCCTTCAGAAAGGCACAGACCACAG
CTATACCCTTCAAAAAAATTATTATCAGAATCTGCTCAACCTTTGAAAAAACTGGAGGAAGAACAAGAGGTGGATAAAGA
AGATGTTTCAGAAGAAGCCAAAAGTAAAGAAGGAACAAAGACTTTCCACAGAATGCCATAAGACAATACTCTCTCGGTCC
ATCACTGGCCACAGATAAATCC

Alignment

ORF - retro_nleu_1976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.99 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APSGSLAVPL-AVLVLLLWSAPWTHGRRSNVRVITDENWRELLEGDWMIEFYAPWCPACQNLQPEWESFA
          APS.SLAVPL.AVLVLLLW.APWTH...SN.R.ITD.NWR.LLEGDWMIEFYAPWCPACQNLQ.EWESFA
Retrocopy APSRSLAVPL<AVLVLLLWGAPWTHRWQSNIRIITDKNWRKLLEGDWMIEFYAPWCPACQNLQLEWESFA

Parental  EWGEDL-EVNVAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFISDKEWKSIEPVS
          EWGEDL.EVNV.KVDVTEQPGL.G.F.ITALPTIYHCKDGEFR..QGPRTKKDFINFISDKEWKSIEPVS
Retrocopy EWGEDL<EVNVVKVDVTEQPGLTGQFTITALPTIYHCKDGEFRHPQGPRTKKDFINFISDKEWKSIEPVS

Parental  SWFGPGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFALATLFSGLSLGLCMIFVADCLCPS
          SWFGPGSV.MSSMSALFQLS.WIRTCHNYFIEDL.LPVWGSYTVF.LATL.SGL.LGLCMIF.ADCLCPS
Retrocopy SWFGPGSVQMSSMSALFQLSLWIRTCHNYFIEDLELPVWGSYTVFPLATLHSGLLLGLCMIFAADCLCPS

Parental  KRRRPQPYPYPSKKLLSEPAQPLKKVEEEQEADEDVSEEEAESKEGTNKDFLQ-NAIRQRSLGPSLATDK
          .R.RPQ...YPSKKLLSE.AQPLKK.EEEQE.D.....EEA.SKEGT.K.F...NAIRQ.SLGPSLATDK
Retrocopy ERHRPQ--LYPSKKLLSESAQPLKKLEEEQEVDKEDVSEEAKSKEGT-KTFHR<NAIRQYSLGPSLATDK

Parental  S
          S
Retrocopy S

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_1976 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976 , retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058, retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,