RetrogeneDB ID: retro_ggor_2400

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:7720132..7720759(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSGGOG00000012619
• Aliases: None
• Description: Isocitrate dehydrogenase [NADP] [Source:UniProtKB/TrEMBL;Acc:G3RA53]

Sequence

>retro_ggor_2400
TCTAAGTGTTGGCCTTTGTAGCTGAGCACCAAAAACACTATTCTGAAGAAATAGGATGGACATTTTAAAGACATCTTTCA
GGAGATATATGACAAGCAGTACAAGTCCCAGTTTGAAGCCCAAAAGATCTGGTATGAGCATAGGCTCATTGATGACATGG
TGGCCCAAGCTATGAAATCAGAAGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGACATGCAGTCAGACTCTGTG
GCCCAAGGGTATGGTTCTCTTGGCATGATGACCGGCATGCTGGTGTGTCCACATGGCAAGACAGTAGAAGCAGAGGCTGC
CCACTGGACTGTAACCCGTCACTACTGCATGTACCAGAAAGGCCAGGAGATATCCACCAATCCCATTGCTTCCATTTTTG
CCTGGACCAGAGGGTTGGCCCTCCAAGCAAAGACTGATAACAATAAAGAGCTCGCCTTTTTTGCAAATGCTTTGGAAGAA
GTCTGTATTGAGACAATTGAGGCTAGTTTCATGACCAAGGACTCGGCTGCTTGCATTAAAGGTTTACCCAGTGCGCAATA
CTTGAATACTTTTGAGTTCATGGACAAACTTGGAGAAAACTTGAAGATCAAACTGGCTCAGGCCAAA

Alignment

ORF - retro_ggor_2400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.15 %
• Parental protein coverage: 51.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKSWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKN
          SK.WPL.LSTKNTILKK.DG.FKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKN
Retrocopy SKCWPL*LSTKNTILKK*DGHFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKN

Parental  YDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLA
          YDGD.QSDSVAQGYGSLGMMT..LVCP.GKTVEAEAAH.TVTRHY.MYQKGQE.STNPIASIFAWTRGLA
Retrocopy YDGDMQSDSVAQGYGSLGMMTGMLVCPHGKTVEAEAAHWTVTRHYCMYQKGQEISTNPIASIFAWTRGLA

Parental  HRAKLDNNKELAFFANALEEVSVETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQ
          ..AK.DNNKELAFFANALEEV..ETIEA.FMTKD.AACIKGLP..Q...YLNTFEFMDKLGENLKIKLAQ
Retrocopy LQAKTDNNKELAFFANALEEVCIETIEASFMTKDSAACIKGLPSAQ---YLNTFEFMDKLGENLKIKLAQ

Parental  AK
          AK
Retrocopy AK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	19.71 RPM
SRP007412_cerebellum	0.00 RPM	14.38 RPM
SRP007412_heart	0.00 RPM	7.97 RPM
SRP007412_kidney	0.00 RPM	138.37 RPM
SRP007412_liver	0.00 RPM	154.68 RPM
SRP007412_testis	0.52 RPM	211.86 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2400 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3554
Pan troglodytes	retro_ptro_2415

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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,