RetrogeneDB ID: retro_nleu_2067

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397326.1:4638170..4638857(+)
• Located in intron of: ENSNLEG00000006047

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSNLEG00000000656
• Aliases: None
• Description: None

Sequence

>retro_nleu_2067
GAGTCCATGAAGACAGTAACAGGGACGGATGTGGAACTGACTGTTGGAGAAAGAAACCTTCCATCTGTTGCATGTAAGAA
TGGGATTGGAGCTACAAGGGCCTCCTGGATAATAATCAGCTGCATTGAACAGGAAGAAGAAAACAAGGGAGGAGAAGACA
GGTGAGGAATGATTTGGGGATATTGGCAAATGGTTGAGACTGAGCTAACAATCTGTTGTGACATTCTGGATGTACTGGAC
AAACCCTGCATTCCAGCAGCTAACACTGGTGAGTCCAAGGTTTTCTATTATAAAAATGAAAGGGGACTACCACAGGTATC
TGGCAGAATTTGCCACAGAAAATGACAGGAAGGAGGCTGCAGAAAACAGTCTAGTGGCTGATATAGCTGTTAATGATATT
GCATTGACAGAACTTCCACCATCGCATCCTATCCGCTTAGGTCTTGCTCTCAATTGTTCCATATTCTACTAGGAAATTCT
TAATTCCCCTGATCATGCCTGCAGGTTGGCAAAGGCAGCTTTGGATAATGCATTGCAGAACTGGATACGCTGAGTTAAGA
AAGCTGTAAGGACTCTACACTTACCATGCAGTTGTTTCATGATAATCTGACACTATGGACTTTGGACATGCAGGGTAATG
GTGAAGAGTAGAATAAAGAAGCTCTGCAAGACGTGGAAGACTCAAGT

Alignment

ORF - retro_nleu_2067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 81.85 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELK
          ESMK.V.G.DVELTV.ERNL.SVA.KN.IGA.RASW.IIS.IEQ.EENKGGED...MI..Y.QMVETEL.
Retrocopy ESMKTVTGTDVELTVGERNLPSVACKNGIGATRASWIIISCIEQEEENKGGEDR*GMIWGYWQMVETELT

Parental  LICCDILDVLDKHLIPAANTGESKVFYY-KMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTEL
          .ICCDILDVLDK..IPAANTGESKVFYY.KMKGDYHRYLAEFAT.NDRKEAAENSLVA..A..DIA.TEL
Retrocopy -ICCDILDVLDKPCIPAANTGESKVFYY>KMKGDYHRYLAEFATENDRKEAAENSLVADIAVNDIALTEL

Parental  PPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDA-IAELDTLSEESYKDSTLIMQLLRDNLTLWT
          PP.HPIRLGLALN.S.FY.EILNSPD.ACRLAKAA.D.A.IAELDTLS.ES.KDSTL.MQL..DNLTLWT
Retrocopy PPSHPIRLGLALNCSIFY*EILNSPDHACRLAKAALDNA<IAELDTLS*ESCKDSTLTMQLFHDNLTLWT

Parental  SDMQGDGEEQNKEVLQDVEDEN
          .DMQG.GEE.NKE.LQDVED..
Retrocopy LDMQGNGEE*NKEALQDVEDSS

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_2067 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 17 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Monodelphis domestica	ENSMODG00000010174	2 retrocopies	retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067 , retro_nleu_2868,
Nomascus leucogenys	ENSNLEG00000003220	7 retrocopies	retro_nleu_1368, retro_nleu_1426, retro_nleu_2186, retro_nleu_23, retro_nleu_449, retro_nleu_487, retro_nleu_722,
Nomascus leucogenys	ENSNLEG00000006643	2 retrocopies	retro_nleu_42, retro_nleu_422,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,