RetrogeneDB ID: retro_nleu_1001

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:31905365..31905766(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1ORF123
• Ensembl ID: ENSNLEG00000017988
• Aliases: None
• Description: None

Sequence

>retro_nleu_1001
CAGTGGTACCTGAAAATGAAACGTGGCAATGGTAGTGAGATTTCAGAGAAGCGGCACTACATCCACCTGATGGATGGTGT
GGCACTAAAGTGGGGCCATGGCAGCTCCTTCATAGCCCAGAAGTGCAAGCTGTGCACACAGGAAACTCCACTGAGATTTT
GAGTGGCACCATCAAATCTTACAATGCCAAAGACAGAGAGAAGTTCAAAACTATAATAGAGTTTGAGTGCCAGGGCTTCA
AACCATTTGATTTCCAGCCCTAGGCTGGGTTTGCTGCTGAGGGCACAAAGTCAAAGACAGTCTTTGGTGACATTCTGCAG
GAGAAAGACCGGACTGACTATGACAAAAAGTCCAGGGAGTCTGTGGGAATCTCTGAGGCCATGCAGCAGTTTTTGAAGTG
C

Alignment

ORF - retro_nleu_1001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.18 %
• Parental protein coverage: 84.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RWYLKMKCGNCGEISDKWQYIRLMDSVALKGGRGSASMVQKCKLCARE-NSIEILSSTIKPYNAEDNE-F
          .WYLKMK.GN..EIS.K..YI.LMD.VALK.G.GS....QKCKLC..E.NS.EILS.TIK.YNA.D.E.F
Retrocopy QWYLKMKRGNGSEISEKRHYIHLMDGVALKWGHGSSFIAQKCKLCTQE<NSTEILSGTIKSYNAKDREKF

Parental  KTIVE-ECRGLEPVDFQPQAGFAAEGVESGTAFSDINLQEKDWTDYDEKAQESVGIYEVTHQFVKC
          KTI.E.EC.G..P.DFQP.AGFAAEG..S.T.F.DI.LQEKD.TDYD.K..ESVGI.E...QF.KC
Retrocopy KTIIEFECQGFKPFDFQP*AGFAAEGTKSKTVFGDI-LQEKDRTDYDKKSRESVGISEAMQQFLKC

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_1001 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001 ,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351, retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999, retro_rnor_2403, retro_rnor_2705,