RetrogeneDB ID: retro_nleu_394

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:35935423..35936347(+)
• Located in intron of: ENSNLEG00000017825

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSNLEG00000013540
• Aliases: None
• Description: None

Sequence

>retro_nleu_394
TGTGTGCCTGTGGACTTTGAGGGAGTGTCAGTGACCTCTACCTCTGCCTCACACGAAGAGGAAATTCACAATGCCATCAT
GGCAGTTCGTTGGAACCATGTGGCTTTGAAGAGTAGTATTAAAACTGACGACACCCTGCCACCATCATACAAATCTTTCA
ACAACATGTTGCACATCACTCTAGATCTCTGTGCCAACGTCATTCATTTGAAAAATTTGCCAAATGTGGAGACCTGGCAC
AAGGACGTAGACATCCTAGTTGTTTGGGAAAACACAGAGGGTGAGTATAGCAATCTGGAGCATGAGAGTGTGAAAGGAGT
GACAGAGAGCCTAAAGATCATGACTAAGGCCAAGTCTTTGCGCATTGCTGAATATGCCTTCCAGCTGGCCCAGAAGATGG
GATGCAAAAAAGTGATGGCTGTGCACAAGGTCAACATCGTGAAACTGGGAGATGGTCTCTTCCTCCAGTGCTGTGGGGAA
GTGGCATCCCACTATCCTCAGCTCACCTTAGAAGACATGATTGTGGAGAATGCCACAATGCAGTGAGTATCCCAGCCCCA
ACATTTTGATGTCATGGTAATGCTCAGTCTTTATGGCAATATTATCAACAGTGTCTTCACAGGTTTGATTGGTGGGGCAG
GCCTTGTGCCTAGAGCCAACTATGTCTATATGTATGCAGTGTTTGAGACAGCTTCAAGGCAATCTGACAATTTAGTCAAT
ACAAATCTGGTAAACCCTACTGCCATGCTGCTGGCAATTTGCATCATGCTGGATTACCTCAAACTCCACTCCTATGCCAC
CCACATTCATACTGCAGTCTTGGCATCTTTGGACAACAAAAGTATCCACACCGCAGACCTTGGAGGCCAGGATACCACAT
TGGGCATCATTCAAAACATCATAGACCACATTCGAAATGTCAAT

Alignment

ORF - retro_nleu_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.31 %
• Parental protein coverage: 78.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CVPVDFEEVHVSSNA--DEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHC
          CVPVDFE.V.V.S.....EE.I.NAIMA.R.N.VALK..I.T...LPPS.KS.NN.L...LDL.ANVIH.
Retrocopy CVPVDFEGVSVTSTSASHEEEIHNAIMAVRWNHVALKSSIKTDDTLPPSYKSFNNMLHITLDLCANVIHL

Parental  KSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQESGRKKVTA
          K.LP.V.T.HKD.DIL.V.ENTEGEYS.LEHESV.GV.ESLKI.TKAKSLRIAEYAF.LAQ..G.KKV.A
Retrocopy KNLPNVETWHKDVDILVVWENTEGEYSNLEHESVKGVTESLKIMTKAKSLRIAEYAFQLAQKMGCKKVMA

Parental  VHKANIMKLGDGLFLQCCREVAARYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLV
          VHK.NI.KLGDGLFLQCC.EVA..YPQ.T.E.MIV.N.TMQ.VS.PQ.FDVMVM..LYGNI.N.V..GL.
Retrocopy VHKVNIVKLGDGLFLQCCGEVASHYPQLTLEDMIVENATMQ*VSQPQHFDVMVMLSLYGNIINSVFTGLI

Parental  GGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVLASMDN
          GG.GLV..ANY...YAVFETA.R.......N.N..NPTA.LLA.C.MLD.LKLHSYAT.I..AVLAS.DN
Retrocopy GGAGLVPRANYVYMYAVFETASRQS-DNLVNTNLVNPTAMLLAICIMLDYLKLHSYATHIHTAVLASLDN

Parental  ENMHTPDIGGQGTTSEAIQDIIRHIRVIN
          ...HT.D.GGQ.TT...IQ.II.HIR..N
Retrocopy KSIHTADLGGQDTTLGIIQNIIDHIRNVN

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_394 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	ENSAMEG00000018466	1 retrocopy	retro_amel_1892,
Bos taurus	ENSBTAG00000001059	1 retrocopy	retro_btau_1194,
Canis familiaris	ENSCAFG00000019286	1 retrocopy	retro_cfam_1023,
Callithrix jacchus	ENSCJAG00000011185	1 retrocopy	retro_cjac_1597,
Equus caballus	ENSECAG00000018509	1 retrocopy	retro_ecab_941,
Homo sapiens	ENSG00000067829	1 retrocopy	retro_hsap_759,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Loxodonta africana	ENSLAFG00000006904	1 retrocopy	retro_lafr_560,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Mustela putorius furo	ENSMPUG00000008781	1 retrocopy	retro_mputfur_644,
Mus musculus	ENSMUSG00000002010	1 retrocopy	retro_mmus_134,
Nomascus leucogenys	ENSNLEG00000013540	1 retrocopy	retro_nleu_394 ,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Pteropus vampyrus	ENSPVAG00000013163	1 retrocopy	retro_pvam_373,
Rattus norvegicus	ENSRNOG00000037284	1 retrocopy	retro_rnor_209,
Sus scrofa	ENSSSCG00000012783	1 retrocopy	retro_sscr_662,
Tursiops truncatus	ENSTTRG00000011728	1 retrocopy	retro_ttru_848,