RetrogeneDB ID: retro_ptro_2415

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:7569707..7570346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSPTRG00000012865
• Aliases: None
• Description: Isocitrate dehydrogenase [NADP] [Source:UniProtKB/TrEMBL;Acc:H2QJB5]

Sequence

>retro_ptro_2415
TCTAAGGATTGGCCTTTGTAGCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGACGTTTTAAAGACATCTTTCA
GGAGATATATGATAAGCAGTACAAGTCCCAGTTTGAAGCCCAAAAGATCTGGTATGAGCATAGGCTCGCTGATGACATGG
TGGCCCAAGCTATGAAATCAGAAGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGACATGCAGTCAGACTCTGTG
GCCCAAGGGTATGGCTCTCTTGGCATGATGACCAGCATGCTGGTGTGTCCACATGGCAAGACAGTAGAAGCAGAGGCTGC
CCACTGGACTGTAACCCGTCACTACTGCATGTACCAGAAAGGCCAGGAGATATCCACCAATCCCATCGCTTCCATTTTTG
CCTGGACCAGAGGGTTGGCCCTCCAAGCAAAGACTGATAACAATAAAGAGCTTGCCTTTTTTGCAAATGCTTTGGAAGAA
GTCTGTATTGAGACAATTGAGGCTGGTTTCATGACCAAGGACTTGGCTGCTTGCATTAAAGGTTTACCCAGTGCGCAATG
TTCTGACTACTTGAATACTTTTGAGTTCATGGACAAACTTGGAGAAAACTTGAAGATCAAACTGGCTCAGGCCAAACTT

Alignment

ORF - retro_ptro_2415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKRYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKN
          SK.WPL.LSTKNTILKKYDGRFKDIFQEIYDK.YKSQFEAQKIWYEHRL.DDMVAQAMKSEGGFIWACKN
Retrocopy SKDWPL*LSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLADDMVAQAMKSEGGFIWACKN

Parental  YDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLA
          YDGD.QSDSVAQGYGSLGMMTS.LVCP.GKTVEAEAAH.TVTRHY.MYQKGQE.STNPIASIFAWTRGLA
Retrocopy YDGDMQSDSVAQGYGSLGMMTSMLVCPHGKTVEAEAAHWTVTRHYCMYQKGQEISTNPIASIFAWTRGLA

Parental  HRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQ
          ..AK.DNNKELAFFANALEEV.IETIEAGFMTKDLAACIKGLP..Q.SDYLNTFEFMDKLGENLKIKLAQ
Retrocopy LQAKTDNNKELAFFANALEEVCIETIEAGFMTKDLAACIKGLPSAQCSDYLNTFEFMDKLGENLKIKLAQ

Parental  AKL
          AKL
Retrocopy AKL

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	11.96 RPM
SRP007412_cerebellum	0.00 RPM	13.80 RPM
SRP007412_heart	0.00 RPM	15.13 RPM
SRP007412_kidney	0.03 RPM	117.34 RPM
SRP007412_liver	0.00 RPM	107.73 RPM
SRP007412_testis	0.00 RPM	43.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2415 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2415 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3554
Gorilla gorilla	retro_ggor_2400

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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,