RetrogeneDB ID: retro_nleu_698

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397270.1:37673697..37674526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSNLEG00000017695
• Aliases: None
• Description: None

Sequence

>retro_nleu_698
TTTCCAGGATGGATTGATAACTTTAATGGACCAAGTGGTCTCTTTATTGTGGCAGGGAAAGGGATTCTTCGAACAATGCA
TGTCTCCAATAATGCCCTTGCAGATCTTGTTCCTGTCGATGTAGTTGTCAACAAGAGTCTTGTGGCAGCCTGGCATTCTG
GAGTTAATAGACCAAGAAACCTCATGTCATATAATTGTACAACAGATAACACTAATCCTTTCCACTGGGGTGAAGTTGAA
CACCATGTAATTTCCACTTTCAAGAGGAATCCTCTCGAACAGGCCTTCAGATGGTCCAATGTAAATCTAACCTCCAATCA
CCTTTTGTATCATTACTGGATTGCTGTAAGCCATAAGGCCTCGGGATTCCTGGATGATATCTACCTCAGAATGACTGGAA
GAAGCCCATGGATGATGAAAGCAATAACTCATCTTCACAAAGCTGTGATGTTACTTGAGTATTTCACAAGTAATTCTTGG
GTTTGGAATACTGAAAATGTCAATATGTTAATGAATCAACTAAACCTTGAAGATAAAAAGACTTTCAAATATTGATGTAC
GGCAGTTACATTGGGCAGAATATATAGAGAACTACTGCATGGGAACTAAGAAGTACATATTTAATTAAGAAATGTCTGGC
CTCCCTACAGCCAGAAAACATCTGAACAAGTTGCAGAATATACCTTATGATTTTAATACTATCCTTGTGATCCTCATCTG
GCACATTTTTATTGCAAGACCACAAATGGCAAGAAACATCTGATACTTTGTGGTTAGTCTGTGTTACAAGTTTCTGTCAT
AGTTTCAAGCATCCAGCACTATGAGATAC

Alignment

ORF - retro_nleu_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.92 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FPGWIDNFNGPSGLFIAAGKGILRTIRASNNALADLVPVDVVVNMSLAAAWYSGVNRPRNIMVYNCTTGS
          FPGWIDNFNGPSGLFI.AGKGILRT...SNNALADLVPVDVVVN.SL.AAW.SGVNRPRN.M.YNCTT..
Retrocopy FPGWIDNFNGPSGLFIVAGKGILRTMHVSNNALADLVPVDVVVNKSLVAAWHSGVNRPRNLMSYNCTTDN

Parental  TNPFHWGEVEYHVISTFKRNPLEQAFRRPNVNLTSNHLLYHYWIAVSHKAPAFLYDIYLRMTGRSPRMMK
          TNPFHWGEVE.HVISTFKRNPLEQAFR..NVNLTSNHLLYHYWIAVSHKA..FL.DIYLRMTGRSP.MMK
Retrocopy TNPFHWGEVEHHVISTFKRNPLEQAFRWSNVNLTSNHLLYHYWIAVSHKASGFLDDIYLRMTGRSPWMMK

Parental  TITRLHKAMVFLEYFTSNSWVWNTDNVNMLMNQLNPEDKKTF-NIDVRQLHWAEYIENYCLGTKKYVLNE
          .IT.LHKA...LEYFTSNSWVWNT.NVNMLMNQLN.EDKKTF.NIDVRQLHWAEYIENYC.GTKKY..N.
Retrocopy AITHLHKAVMLLEYFTSNSWVWNTENVNMLMNQLNLEDKKTF>NIDVRQLHWAEYIENYCMGTKKYIFN*

Parental  EMSGLPAARKHLNKLRNIRYGFNTILVILIWRIFIARSQMARNIWYFVVSLCYKFLSYFRASSTMRY
          EMSGLP.ARKHLNKL.NI.Y.FNTILVILIW.IFIAR.QMARNI.YFVVSLCYKFLS.F.ASSTMRY
Retrocopy EMSGLPTARKHLNKLQNIPYDFNTILVILIWHIFIARPQMARNI*YFVVSLCYKFLS*FQASSTMRY

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_698 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003490	2 retrocopies	retro_chof_1358, retro_chof_1733,
Callithrix jacchus	ENSCJAG00000010077	1 retrocopy	retro_cjac_545,
Cavia porcellus	ENSCPOG00000002654	1 retrocopy	retro_cpor_267,
Homo sapiens	ENSG00000197601	1 retrocopy	retro_hsap_1225,
Gorilla gorilla	ENSGGOG00000001180	1 retrocopy	retro_ggor_958,
Macaca mulatta	ENSMMUG00000011990	1 retrocopy	retro_mmul_1301,
Nomascus leucogenys	ENSNLEG00000017695	1 retrocopy	retro_nleu_698 ,
Oryctolagus cuniculus	ENSOCUG00000004336	2 retrocopies	retro_ocun_1056, retro_ocun_790,
Otolemur garnettii	ENSOGAG00000005064	2 retrocopies	retro_ogar_1353, retro_ogar_341,
Pongo abelii	ENSPPYG00000003470	1 retrocopy	retro_pabe_1019,
Pan troglodytes	ENSPTRG00000024190	1 retrocopy	retro_ptro_840,
Rattus norvegicus	ENSRNOG00000013176	1 retrocopy	retro_rnor_467,