RetrogeneDB ID: retro_nleu_50

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397393.1:2243544..2244480(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018190
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSNLEG00000007376
• Aliases: None
• Description: None

Sequence

>retro_nleu_50
ATGGACTTAAAACTAAAAGATTGTGAATTTTGGTACAGTCTCCATGGCCAGGTCCCAGGGCTGCTGGACTGGGACATGGG
GAATGAGTTACTTTTGCCTTGTATTACAGACCAGTGCTCTTTAGCTGAGCAGATCCTTGCCAAATACAGAGTCCGAGTAA
TGAAGCCCCCAGAGATGCCTCAGAAGAGGAGACCCAGTCCTGATGAAGATGGTCCTCACTGTGAACCCAATCTGTGGATG
TGGGTGGACCCCAATATCCTGTGCCCCCTTGGCAGCCAGGAGGCCCCAAAGCCCAGTGGAAAAGAGGATCTGACAAATAT
TTCTCCTTTCCCTCAGCCCCCACTAAAAGATGAAGAGTCTAACTGCTCAGAGGACAAAGTGGTAGAGTCTCTGCCATCTT
CCTGCAGTAAGCAGTCTCCTTTAAAGAAGCAGGATATTCATTCCCCCAGTGACTTTGAGCCCACAGAAGAGGAGGCTGAG
GAACAAGAGGACAACTCCCTCCAGTCCCCTGAAAGAAAGTGCTTCCAGAGCCAAAAACTATGGCAAATCAACAGCCAAGA
GAAGTCCTGGCAAAGGCCCCCTCTCAATTGTAGCCACCTTATTGCTCTAGCATTAAGAAACAGCCCCCACCGTGGCCTCA
GTGTGCAGGAGATCTACAATTTCACCCGACAGCATTTCCCCTTTCTCTGGATAGCTCCGGATGGCTGGAAGAGCACCATT
CATTACAACCTTTGCTTCCTGGACAGCTTTGAGAAGGTGCCAGACAGCCTTAAGGATGAAGATAATGCAAGACCTCGCTC
TTGCCTTTGGAAGCTCACTAAGGAGGGGCACCGCCGCTTTTGGGAGGAGACTCGTGCCTTAGCCTCTGCTCAAAGGGAGA
GAATCCAAGAGTGCATGAGTCAGCCAGAGTTGTTGACCTCTCTCTTTGATCTTTGA

Alignment

ORF - retro_nleu_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.82 %
• Parental protein coverage: 95.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IARYKLRIVKPPKLPLEKKPNPDKDGPDYEPNLWMWVNPNIVYPPGKLEVPGPKKREDLTSTLPFSQPPQ
          .A.Y..R..KPP..P....P.PD.DGP..EPNLWMWV.PNI..P.G..E.P.P...EDLT...PF.QPP.
Retrocopy LAKYRVRVMKPPEMPQKRRPSPDEDGPHCEPNLWMWVDPNILCPLGSQEAPKPSGKEDLTNISPFPQPPL

Parental  KEEDASCSEATGVESLSRSSSKQSPPRKRFAFSPSTWELTEEEEAEDQEDTSSVALPSPHKRPPLQSRRL
          K.E...CSE...VESL..S.SKQSP..K....SPS..E.TEEE.AE.QED.S...L.SP..R...QS..L
Retrocopy KDEESNCSEDKVVESLPSSCSKQSPLKKQDIHSPSDFEPTEEE-AEEQEDNS---LQSP-ERKCFQSQKL

Parental  RQASSQAGRLWSRPPLNYFHLIALALRNSSPCGLNVQQIYSFTRKHFPFFRTAPEGWKNTVRHNLCFRDS
          .Q..SQ....W.RPPLN..HLIALALRNS...GL.VQ.IY.FTR.HFPF...AP.GWK.T...NLCF.DS
Retrocopy WQINSQE-KSWQRPPLNCSHLIALALRNSPHRGLSVQEIYNFTRQHFPFLWIAPDGWKSTIHYNLCFLDS

Parental  FEKVPVSMQGGASTRPRSCLWKLTEEGHRRFAEEARALASTRLESIQQCMSQPDVMPFLFDL
          FEKVP.S.......RPRSCLWKLT.EGHRRF.EE.RALAS...E.IQ.CMSQP.....LFDL
Retrocopy FEKVPDSLKDEDNARPRSCLWKLTKEGHRRFWEETRALASAQRERIQECMSQPELLTSLFDL

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_50 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50 ,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,