RetrogeneDB ID: retro_nleu_3117

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL400151.1:3935..5171(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018692
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_nleu_3117
ATGTCCAAAAAAATCAGTGGCGGTTCTGTGGTAGAGATGCAAGATGAAATGACACGAATCATTTGGGAATTGATTAAAGA
GAAACTCATTTTTCCCTACGTGGAATTAGATCTACATAGCTATGATTTAGGCATAGAGAATCGTGATGCCACCAACGACC
AAGTCACCAAGGTTGCTGCAGAAGCTATAAAGAAGTATAATGTTGGCGTCAAATGTGCCACTATCACTCCTGATGAGAAG
AGGGCTGAGGAGTTCAAGTTGAAACAAATGTGGAAATCACCAAATGGCACCATACGAAATATTCTGGGTGGCACGGTCTT
CAGAGAAGCCATTATCTGCAAAAATATCCCCTGGCTTGTGAGTGGATGGGTAAAACCTATCATCATAGGTCGTCATGCTT
ATGGGGATCAATACAGAGCAAATGATTTTGTTGTTCTGGCTGGAAAGGTAGAGATAACCTACACACCAAGTGACGGAACC
CAAAAGGTGACATACCTGGTACATAACTTTGAAGAGGGTGGTGGTGTTGCCATGGGAATGTATAATCAAGATAAGTCAAT
TGAAGATTTTGCACACAGTTCCTTCCAGATGGCTCTGTCTAAGGGTTGGCCTTTGTATGTGAGCACCAAAAACACTATTC
TGAAGAAATATGATGGGCGTTTTAAAGACATCTTTCAGGAGATATATGACAAGCAGTACAAGTCCCAATCTGAAGGCCAA
AAGATCTGGTATGAGCATAGGCTCATCGATGACACGGTGGCCCAAGCTATGAAATCAGAGGGAGGCTTCATCTGGGCCTG
TAAAAACTATGATGGTGACACGCAGTCAGACTCTGTGGCCCAAGGGTATGGCTCTCTCGGCATGATGACCAGCGTGCTGG
TTTGTCCAGATGGCAAGACAGTAGAAGCAGAGGCTGTCCAAGGGACTGTAACCTGTCACTACCACATGTACCAGAAAGGA
CAGGAGACGGCCACCAATCCCATTGCTTCCATTTTTGCCTGGACCAGAGGGTTAGCCCACAGAGCAAAGCTTGATAACAA
TAAAGAGCTTGCCTTCTTTGCAAATGCTTTGGAAGAAGTCTCTATTGAGACAATTGAGGCTGGCTTCATGACCAAGGACT
TGGCTGCTTGCATTAAAGGTGTACCCAATGTACAACGTTCTGACTACTTGAATACGCTTGAGTTCATGGACAAACTTGGA
GAAAACTTGAAGATCAAACTAGCTCAGGCCAAATTA

Alignment

ORF - retro_nleu_3117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVG
          MSKKISGGSVVEMQ.DEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTK.AAEAIKKYNVG
Retrocopy MSKKISGGSVVEMQ-DEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKVAAEAIKKYNVG

Parental  V-CATITPDEKR-EEFKLKQMWKSPNG-HHTKY-FWVAQ-FFREAIIC-NIPRLVSGWVKPIIIGRHAYG
          V.CATITPDEKR.EEFKLKQMWKSPNG.HHTKY.FWVA...FREAIIC.NIP.LVSGWVKPIIIGRHAYG
Retrocopy VKCATITPDEKRAEEFKLKQMWKSPNG<HHTKY<FWVAR<VFREAIICKNIPWLVSGWVKPIIIGRHAYG

Parental  DQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWP
          DQYRA.DFVV...GKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWP
Retrocopy DQYRANDFVVLA-GKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWP

Parental  LYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDV
          LY.STKNTILKKYDGRFKDIFQEIYDKQYKSQ.E.QKIWYEHRLIDD.VAQAMKSEGGFIWACKNYDGD.
Retrocopy LYVSTKNTILKKYDGRFKDIFQEIYDKQYKSQSEGQKIWYEHRLIDDTVAQAMKSEGGFIWACKNYDGDT

Parental  QSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKL
          QSDSVAQGYGSLGMMTSVLVCPDGKTVEAEA..GTVT.HY.MYQKGQET.TNPIASIFAWTRGLAHRAKL
Retrocopy QSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAVQGTVTCHYHMYQKGQETATNPIASIFAWTRGLAHRAKL

Parental  DNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL
          DNNKELAFFANALEEVSIETIEAGFMTKDLAACIKG.PNVQRSDYLNT.EFMDKLGENLKIKLAQAKL
Retrocopy DNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGVPNVQRSDYLNTLEFMDKLGENLKIKLAQAKL

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_3117 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,