RetrogeneDB ID: retro_pabe_2935

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:7754117..7754755(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSPPYG00000013125
• Aliases: None
• Description: Isocitrate dehydrogenase [NADP] cytoplasmic [Source:UniProtKB/Swiss-Prot;Acc:Q5R9C5]

Sequence

>retro_pabe_2935
TCTAAGGGCTGGCCTTTGTAGCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGACGTTTTAAAGACGTCTTTCA
GGAGATATATGACAAGCAGTACAAGTCCCAGTTTGAAGCCCAAAAGATCTGGTATGAGCATAGGCTCATCGAAGACATGG
TGGCCCAAGCTATGAAATCAGAAGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGACATGCGGTCAGACTTTGCG
GCCCAAGGGTATGGCTCTCTTGGCATGATGAGCAGCATGCTGGTGTGTCCACATGGCAAGACAGTAGAAGCAGAGGCTGC
CCACTGGACTGTAACCTGTCACTACTGCATGTACCAGAAAGGCCAGGAGACATCCACCAATCCCATTGCTTCCATTTTTG
CCTGGACCAGAGGGTTGGCCCTCAGAGCAAAGACTGATAACAATAAAGAGCTTGCCTTCTTTGCAAATGCTTTGAAAGAA
GTCTGTACTGAGACAATTGAGGCTGGTTTCATGACTAAGGACTTGGCTGCTTGCATTAAAGGTTTACCCAATGTGCAATG
TTCTGACTACTTGAATACGTTTGATTCAAGGACAAATTTGGAGAAAACTTGAAGATCAAACTGGCTCAGGCCAAACTT

Alignment

ORF - retro_pabe_2935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.79 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEARKIWYEHRLIDDMVAQAMKSEGGFIWACKN
          SKGWPL.LSTKNTILKKYDGRFKD.FQEIYDKQYKSQFEA.KIWYEHRLI.DMVAQAMKSEGGFIWACKN
Retrocopy SKGWPL*LSTKNTILKKYDGRFKDVFQEIYDKQYKSQFEAQKIWYEHRLIEDMVAQAMKSEGGFIWACKN

Parental  YDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLA
          YDGD..SD..AQGYGSLGMM.S.LVCP.GKTVEAEAAH.TVT.HY.MYQKGQETSTNPIASIFAWTRGLA
Retrocopy YDGDMRSDFAAQGYGSLGMMSSMLVCPHGKTVEAEAAHWTVTCHYCMYQKGQETSTNPIASIFAWTRGLA

Parental  HRAKLDNNKELAFFANALEEVSVETIEAGFMTKDLAACIKGLPNVQRSDYLNTFE-FMDKLGENLKIKLA
          .RAK.DNNKELAFFANAL.EV..ETIEAGFMTKDLAACIKGLPNVQ.SDYLNTF..F.DK.GENLKIKLA
Retrocopy LRAKTDNNKELAFFANALKEVCTETIEAGFMTKDLAACIKGLPNVQCSDYLNTFD<FKDKFGENLKIKLA

Parental  QAKL
          QAKL
Retrocopy QAKL

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	14.54 RPM
SRP007412_cerebellum	0.00 RPM	15.20 RPM
SRP007412_heart	0.00 RPM	34.41 RPM
SRP007412_kidney	0.03 RPM	172.33 RPM
SRP007412_liver	0.00 RPM	148.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2935 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2935 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2935 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1817

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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,