RetrogeneDB ID: retro_nleu_2511

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397364.1:3479343..3480034(-)
• Located in intron of: None

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_2511
AGGTGTTGAGCCCAACACATCGTACCCTGTACTATATCTAAGCTGCTTTCTGCCACTTTGATTGATGAAGTGGTTAAAAT
TGGGAATGTTGAGATTTCACAGTCGCTATTGTGGGGGATCATCCAACATGCAGAGAAGGCTCCAACCAATACTGTTTACA
AAATAGATGACATGACAATTGCACCTATGGATGTTCGCCAGTGGGTTGACACAGATGACACCAACAGTGAATACACTGTC
ATTCCTCCAGAAAAATATGTCACTGTGGCAGGCTATTTGAGACCTTTTCAGGACAAAAAGAGCCTGGTACCCTTTAAAAT
CATGCCCCAGAGGATATGAATAAATTCACCACCCATATTCTGGAAGTGATCAATGTACACATGATACTAAGCAAAGATAA
CAGGGAGCCCTCAGCAAGGAGAGCATCTATCAGCAATCCAGGAATGAGTGAAGCAGGGAAATTTGGTGGGAATAGCTTCA
TGCCAGCAAAGGACCTACTGTGGCCCAAAACCAGGTGTTGAATTTGATTAAGGGTTGCCCAAGACCCAAAGAATTGAACT
TTCAGGATCTCAAGAACCAGCTCGACCACATGTCTGTATCCTCAACCAATCAAGCTGTGGATTTTCTGAGCAATGGGGGG
CACAGCTATTCTACTGTGGATGATTATCATTTTAAATCCACAAATGCAGAA

Alignment

ORF - retro_nleu_2511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.83 %
• Parental protein coverage: 65.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RARAQHIVPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVD
          R..AQHIVPCTIS.LLSATL.DEV..IGNVEISQ....GII.HAEKAPTN.VYKIDDMT.APMDVRQWVD
Retrocopy RC*AQHIVPCTISKLLSATLIDEVVKIGNVEISQSLLWGIIQHAEKAPTNTVYKIDDMTIAPMDVRQWVD

Parental  TDDASSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPL-EDMNEFTTHILEVINAHMVLSKANSQPSA
          TDD..SE.TV.PPE.YV.VAG.LR.FQ.KKSLV.FKIMP..EDMN.FTTHILEVIN.HM.LSK.N..PSA
Retrocopy TDDTNSEYTVIPPEKYVTVAGYLRPFQDKKSLVPFKIMPQ<EDMNKFTTHILEVINVHMILSKDNREPSA

Parental  GRAPISNPGMSEAGNFGGNSFMPA-NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVD
          .RA.ISNPGMSEAG.FGGNSFMPA..G.TVAQNQVLNLIK.CPRP..LNFQDLKNQL.HMSVSS..QAVD
Retrocopy RRASISNPGMSEAGKFGGNSFMPA<KGPTVAQNQVLNLIKGCPRPKELNFQDLKNQLDHMSVSSTNQAVD

Parental  FLSNEGHIYSTVDDDHFKSTDAE
          FLSN.GH.YSTVDD.HFKST.AE
Retrocopy FLSNGGHSYSTVDDYHFKSTNAE

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_2511 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,