RetrogeneDB ID: retro_nleu_1119

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:19401030..19401832(+)
• Located in intron of: ENSNLEG00000012491

Retrocopy information

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

Parental gene information

• Parental gene symbol: ODC1
• Ensembl ID: ENSNLEG00000013820
• Aliases: None
• Description: None

Sequence

>retro_nleu_1119
TTCCTTGATGAAGGTTTTACTGCCAAGGACATTCTGGACCAAAAAATTAATGAATTTTCTTCTGATGATGATTAGGATGC
CTTCTATGTCACGGACCTTAGAGACATTCTAAAGACACATCTAAGATGGTTAAAAGCTCTTCCTCATGTCACCCCCTTTT
ATGCAGTCAAATATAATGACAACAGAGCCATCATGAAGACTCTTGCTGCCATCGGGACAGGATTTGACTGTGCTAGCAAG
GCTGAAATACAATTGGTGCAGATTCTGGGGATGCCCCCAGAGAGGTTTATCTACGCAAATTCTTGTAAACAAATGTCTCA
AATTAAGTGCACTGCCAATAATGGAGTCCAGATGATGATTTTCGGTAATGAGGTCAAGTTCATGTCAGTTGCCAGAACAC
ACTCAAAGCAGAGTTGGTTTTTAAGATTGCAAATGATAATTCCAAAGCAGCCCGTCACGTCAGTGTTAAATCTGGTGCCA
TGCTCAAAGCCAGCAGGCTTCTTTTGGAATGGGCAAAAGAGCCAAATATTGATGTCACTGGTGTCAGCTTCCATGCAGGA
AGTAGCTGTACCAATCTTGAGACCTTCATGCAGGCAGCCTCCAATGTCCATTGTGTCTTTGACACAGGAGTTGAGTTTGG
TTTCAGAATGTAACTGCTTAATACTGGCAGTTGCTTTCCTGGATCTGAGGATGTGAGGCTTAAATTTGAAGTATTACCAG
TGTAATCAACCCAGCATCGGACAAGTATTTTCCACCAGACTCTAGAGTGAGAGTCACAGCTGAGCCAGGCAGATATTTCA
TG

Alignment

ORF - retro_nleu_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.96 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAA
          FLDEGFTAKDILDQKINE.SS.DD.DAFYV.DL.DILK.HLRWLKALP.VTPFYAVK.ND..AI.KTLAA
Retrocopy FLDEGFTAKDILDQKINEFSSDDD*DAFYVTDLRDILKTHLRWLKALPHVTPFYAVKYNDNRAIMKTLAA

Parental  IGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHP-KAKL
          IGTGFDCASK.EIQLVQ.LG.PPER.IYAN.CKQ.SQIK..ANNGVQMM.F..EV..M.VAR.H..KA.L
Retrocopy IGTGFDCASKAEIQLVQILGMPPERFIYANSCKQMSQIKCTANNGVQMMIFGNEVKFMSVARTHS<KAEL

Parental  VLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDM
          V..IA.D.SKA....SVK.GA.L..SRLLLE.AKE.NIDV.GVSFH.GS.CT..ETF.QA.S...CVFD.
Retrocopy VFKIANDNSKAARHVSVKSGAMLKASRLLLEWAKEPNIDVTGVSFHAGSSCTNLETFMQAASNVHCVFDT

Parental  GAEVGFSMYLLDIGGGFPGSEDVKLKFE-EITGVINPALDKYFPSDSGVRIIAEPGRYYV
          G.E.GF.M.LL..G..FPGSEDV.LKFE..IT.VINPA.DKYFP.DS.VR..AEPGRY..
Retrocopy GVEFGFRM*LLNTGSCFPGSEDVRLKFE<SITSVINPASDKYFPPDSRVRVTAEPGRYFM

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_1119 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 10 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119 ,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,