RetrogeneDB ID: retro_nleu_2328

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397343.1:7511643..7512822(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSNLEG00000007143
• Aliases: None
• Description: Isocitrate dehydrogenase [NADP] [Source:UniProtKB/TrEMBL;Acc:G1R682]

Sequence

>retro_nleu_2328
CAAATCATTTGGGAATTGATTAAAGAGAAACTCATTTTTCCCTATGTGGAATTGGATCTACATAGCTATGATTTAGGCAT
AGAGAACTGTGATGCCACTAATGACCAGGTCACCAAGGATGCTGTAGAAGCTATAAAGAAGTACAATGTTGGTGTCAAGT
GTGCCACCATCACCGCTGATGAGAAGAGGGTTGAGGAGTTCAAGTTGAAACAAATGTGGAAATCGCCAAATGGCACCATC
CAAAATATTCTGGTTGGCACGGTCTTTGGAGAAGCCATTATCTGCAAAAATATTCCCCAGCTTGTGAGTGGATGGGTAAA
ACCCATCATCGTAGGTCACCATGCTTATGGGGATCAATACAGAGCAGCTGATTTTGTTGTTCCTGGGCCTGGAAATGTAG
AGATAACCTACACACTAAGTGACAGAACCCAAAAGGTGACATATCTGGTACATAACTTGGAAGAGGGTGGTGGTGTTGCC
ATGGGGATGTATAATCAAGATAAGTCAATTGAGGATTTTGCACAGTTCATTCCAAATGGCTCTAAGCATTGGCCTTTGTA
GCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGACATTTTGAAGACATCTTTCAGGAGATATATGACAAGCAGT
ACAAGTCCCAATCTGAAACCCAAAAGATCTGGTATGAGTATAGGCTCATCGATAACATGGTGGCCCCATCTATGAAATCA
GAAGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGGCATGCAGTCAGACTCTGTGGCCCAAGGGTATAGCTCTCC
TGGCATGATGACCAACATGCTGGTGTGTCCACATGGCAAGACAGTAGAAGCAGAGGCTGCCCACTGGACTGTAACCCATC
ACTACTCCATGTACCAGAAAGGCCAGGAGACATCCACCAATCCCATTGCTTCCATTTTTGCCTGGACCAGAGGGTTGGCC
CTCAGAGCAAAGATTGATAACAATAAAGAGCTTGCCTTCTTTGCAAATGCTTTGGAAGAAGTCTGTATTGAGACAATTGA
GGCTGGTTTCATGACCAAGGACTTGGCTGCTTGCATTAAAGGTTTACCCAGTGCGCAATGTTCTGACTACTTGAATAGGT
TTGAGCTCATGGACAAACTTGGAGAAAACTTGAAGATCAAACTGGCTCAGGCCAAACTT

Alignment

ORF - retro_nleu_2328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.46 %
• Parental protein coverage: 95.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGV-CATITPDEKR-EEFKLK
          .IIWELIKEKLIFPYVELDLHSYDLGIEN.DATNDQVTKDA.EAIKKYNVGV.CATIT.DEKR.EEFKLK
Retrocopy QIIWELIKEKLIFPYVELDLHSYDLGIENCDATNDQVTKDAVEAIKKYNVGVKCATITADEKRVEEFKLK

Parental  QMWKSPNG-HHTKY-FWVAQ-FFREAIIC-NIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEIT
          QMWKSPNG.HH.KY.FW.A...F.EAIIC.NIP.LVSGWVKPII.G.HAYGDQYRA.DFVVPGPG.VEIT
Retrocopy QMWKSPNG<HHPKY<FWLAR<VFGEAIICKNIPQLVSGWVKPIIVGHHAYGDQYRAADFVVPGPGNVEIT

Parental  YTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKD
          YT.SD.TQKVTYLVHN.EEGGGVAMGMYNQDKSIEDFA...F....SK.WPL.LSTKNTILKKYDG.F.D
Retrocopy YTLSDRTQKVTYLVHNLEEGGGVAMGMYNQDKSIEDFAQ--FIPNGSKHWPL*LSTKNTILKKYDGHFED

Parental  IFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVL
          IFQEIYDKQYKSQ.E.QKIWYE.RLID.MVA..MKSEGGFIWACKNYDG..QSDSVAQGY.S.GMMT..L
Retrocopy IFQEIYDKQYKSQSETQKIWYEYRLIDNMVAPSMKSEGGFIWACKNYDGGMQSDSVAQGYSSPGMMTNML

Parental  VCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIE
          VCP.GKTVEAEAAH.TVT.HY.MYQKGQETSTNPIASIFAWTRGLA.RAK.DNNKELAFFANALEEV.IE
Retrocopy VCPHGKTVEAEAAHWTVTHHYSMYQKGQETSTNPIASIFAWTRGLALRAKIDNNKELAFFANALEEVCIE

Parental  TIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL
          TIEAGFMTKDLAACIKGLP..Q.SDYLN.FE.MDKLGENLKIKLAQAKL
Retrocopy TIEAGFMTKDLAACIKGLPSAQCSDYLNRFELMDKLGENLKIKLAQAKL

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_2328 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020527	1 retrocopy	retro_btau_1235,
Choloepus hoffmanni	ENSCHOG00000004574	2 retrocopies	retro_chof_2158, retro_chof_897,
Cavia porcellus	ENSCPOG00000013587	1 retrocopy	retro_cpor_1010,
Homo sapiens	ENSG00000138413	1 retrocopy	retro_hsap_3554,
Gorilla gorilla	ENSGGOG00000012619	1 retrocopy	retro_ggor_2400,
Microcebus murinus	ENSMICG00000009797	1 retrocopy	retro_mmur_1364,
Macaca mulatta	ENSMMUG00000016077	1 retrocopy	retro_mmul_1817,
Nomascus leucogenys	ENSNLEG00000007143	3 retrocopies	retro_nleu_1169, retro_nleu_2328 , retro_nleu_3117,
Otolemur garnettii	ENSOGAG00000014848	4 retrocopies	retro_ogar_1488, retro_ogar_2270, retro_ogar_2925, retro_ogar_3057,
Pongo abelii	ENSPPYG00000013125	2 retrocopies	retro_pabe_2935, retro_pabe_926,
Pan troglodytes	ENSPTRG00000012865	1 retrocopy	retro_ptro_2415,
Sus scrofa	ENSSSCG00000023264	1 retrocopy	retro_sscr_549,