RetrogeneDB ID: retro_nleu_250

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:33416679..33417460(+)
• Located in intron of: ENSNLEG00000007147

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSNLEG00000009702
• Aliases: None
• Description: None

Sequence

>retro_nleu_250
GCAGCAACTCATAGGGGAGCCGGTGAATACACGCAGTCCCCGGGAGGCTTTGGATCGCGGGCACCTTCTTAGGCAGAAAA
GAAATCAAGAGCCAGATCACAGCACATTGAACCCCACACTATATCTCAGCTGCTTTCTGCCACTTTGGTTGATGATGTGT
TCAAAATTGGCAATGCTGAGATTTCACAAGTCACTCTTGTGGGGATCATCAGACATGCAGAGAAGGCTTCAACCAACATT
GTTTACAAAATAGATGACATGACAGCTGCACCCGTGGATGTTCGCCGGTGGGTTGTCACAGATGACACCAGCAGTGAAAA
CACTTTAGTTCCTCCAGAAACATATGTGAAAGTGGCAGGCCACCTGAGATCTTTTCAGGACAAAAAGAGCCTGGTAGCCT
TTATAAATCATGCTCCTGGAGGATATGAATTAGTTCACCACACATATTCTGGAAGTGATGGATGCATACATGATACTAAA
CAAAGCGAACAGCCAGCCCTCAGCAGGGAGAGCACCTATCAGCAATCCAGGGAAGAGCGAAGCAGGGTACTTTGGTGAGA
ATAGCTTCATGCCAGCAAATGGCCTCACTGTGGCCCAAAACCAGGTGTTGAATTTGATTAAGTCTTGCCCAAGACCTGAA
GGATTGACCTTTCAGGATCTCAAGAATCAGCTCAAACGCATGTCTATATCCTCAATCAAGCAAGCTGTGGATTTTCTCAG
AAATGAGGGGCACATCTATTCTACTGTGGATGATGATCATTTTAAATCCACAGATGCAGAA

Alignment

ORF - retro_nleu_250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.06 %
• Parental protein coverage: 73.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVEISQVTIVGII
          .....GAG.YTQSPGGFGS.APS.AEKKSRAR.QHI.P.TISQLLSATLVD.VF.IGN.EISQVT.VGII
Retrocopy AATHRGAGEYTQSPGGFGSRAPS*AEKKSRARSQHIEPHTISQLLSATLVDDVFKIGNAEISQVTLVGII

Parental  RHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDASSENTVVPPETYVKVAGHLRSFQNKKSLVAFK-IMPL
          RHAEKA.TNIVYKIDDMTAAP.DVR.WV.TDD.SSENT.VPPETYVKVAGHLRSFQ.KKSLVAF..IM.L
Retrocopy RHAEKASTNIVYKIDDMTAAPVDVRRWVVTDDTSSENTLVPPETYVKVAGHLRSFQDKKSLVAFI>IMLL

Parental  EDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVAQNQVLNLIKAC
          EDMN.FTTHILEV..A.M.L.KANSQPSAGRAPISNPG.SEAG.FG.NSFMPANGLTVAQNQVLNLIK.C
Retrocopy EDMN*FTTHILEVMDAYMILNKANSQPSAGRAPISNPGKSEAGYFGENSFMPANGLTVAQNQVLNLIKSC

Parental  PRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE
          PRPEGL.FQDLKNQLK.MS.SSIKQAVDFL.NEGHIYSTVDDDHFKSTDAE
Retrocopy PRPEGLTFQDLKNQLKRMSISSIKQAVDFLRNEGHIYSTVDDDHFKSTDAE

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_250 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250 , retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,