RetrogeneDB ID: retro_nleu_2534

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397368.1:5213490..5214192(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSNLEG00000005850
• Aliases: None
• Description: cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]

Sequence

>retro_nleu_2534
GTCAACACTCCAGAGGGCTTAGTCTGAGAAGGTGAGATTGCCATGCTTGGTGGTGTAGGAGAAGAGAATAAGAAACTGCG
GAGCTTTACCAAAAAGGCCTTGCACGTTCAGTTGGACAGCATACCAGAAGTACCTTTACTGGTTGATGTGCCTTGTTTAT
CTGCTCAGTTGGATGAGTCTATTCTTAACACCATGAAAGACCACATTCTTAAGCATGGAACAGTAGCATCTCGCCCACCA
GTACAGACAGAAGAACTGATAGAGAAACCTGGAGGCATCATAGTACAGTGGTGTAAGGCGGATGATGACTGTACGGCACA
AGATGACAGGCTCCAGTTTCGTAAATGTATTTCAAATCATTTTGAGGGTGTATATGTAGGTTCCAAAACTGAATTCATAG
TATTGCACACAGAGTCCAACGTTGAAGATCATTTCAGAATCTGCACCCAAAGAGATGGCTGACAGGAGCGGAGTCCTTGG
AGTGTCCCCCAGATAGTTCATTCCATATTGGAGCCTCACGAGTGGACAGCTGGTTTTGAGGGGAACAGTCTAAGCAATCG
AAGAAATACGTCATGCTGGAACGATTCTGAATCTTCAGGTGTTCTCAACTCCAGAGCTTCAACTTATTTCTCTGGGCAGA
TATTAATATTTAGAGTTGAAACTGTGGGACTACCAGACAGAAGAGACAGTATAGGAGTGTGT

Alignment

ORF - retro_nleu_2534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.91 %
• Parental protein coverage: 62.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNTAEDLVREGEIAMLGGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIF
          VNT.E.LV.EGEIAMLGGVGEEN.KL.SFTKKA.H.QLDS.PEVPLLVDVPCLSAQLD.SILN..KDHI.
Retrocopy VNTPEGLV*EGEIAMLGGVGEENKKLRSFTKKALHVQLDSIPEVPLLVDVPCLSAQLDESILNTMKDHIL

Parental  KHGTVASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPN
          KHGTVASRPPVQ.EELIEKPGGIIV.WCK.DDD.TAQD.RLQFRKC.SNHFE.VYVGS.TEFIVLH...N
Retrocopy KHGTVASRPPVQTEELIEKPGGIIVQWCKADDDCTAQDDRLQFRKCISNHFEGVYVGSKTEFIVLHTESN

Parental  VDYQFRVCARGDGRQEWSPWSVPQIGHSTLVPHEWTAGFEGYSLSSRRNIALRNDSESSGVLYSRAPTYF
          V...FR.C...DG.QE.SPWSVPQI.HS.L.PHEWTAGFEG.SLS.RRN....NDSESSGVL.SRA.TYF
Retrocopy VEDHFRICTQRDG*QERSPWSVPQIVHSILEPHEWTAGFEGNSLSNRRNTSCWNDSESSGVLNSRASTYF

Parental  CGQTLTFRVETVGQPDRRDSIGVC
          .GQ.L.FRVETVG.PDRRDSIGVC
Retrocopy SGQILIFRVETVGLPDRRDSIGVC

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_2534 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 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014163	1 retrocopy	retro_cjac_1183,
Homo sapiens	ENSG00000176390	3 retrocopies	retro_hsap_2121, retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla	ENSGGOG00000005002	3 retrocopies	retro_ggor_1644, retro_ggor_1649, retro_ggor_2278,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Mus musculus	ENSMUSG00000017561	1 retrocopy	retro_mmus_368,
Nomascus leucogenys	ENSNLEG00000005850	4 retrocopies	retro_nleu_1957, retro_nleu_2534 , retro_nleu_2899, retro_nleu_2900,
Pongo abelii	ENSPPYG00000008142	3 retrocopies	retro_pabe_1925, retro_pabe_1984, retro_pabe_2672,
Pan troglodytes	ENSPTRG00000008963	2 retrocopies	retro_ptro_1560, retro_ptro_2175,