RetrogeneDB ID: retro_pabe_926

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:54545344..54546525(-)
• 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_926
ATCATTTGGGAATTGATTAAAGAGAAACTCATTTTTCCCTACATGGAATTGGATCTACATAGCTATGATTTAGGCATAGA
GAATCGTGATGCCACCAACGACCAAGTCACCAAGGATGCTGCAGAAGCTATAAAGAAGTATAATGTTGGTGTCAAATGTG
CCACTATCACTCTGACGAGAAGAGGGTTGAGGAGTTCAAGTTGAAACAAATGTGGAAATCACCAAATGGCACCATAAGAA
ATATTCTGGGTGGCACGGTCTTCAGAGAAGCCATTTTCTGCAAAAATATCCCCTGGCTTGTGAGTGGATGGGTAAAACCT
ATCATCATAGGTCATCATGCTTATGGGGATCAATACAGAGCAACTGATTTTGTTGTTCCTGGGCCTGGAAAAGTAGAGAT
AAGCTACACACCAAGTGACGGAACCCAAAAGGTGACATACCTGGTACATAACTTTGAAGAGGGTGGTGGTGTTGCCATGG
GGATGTATAATCAAGATAAGTCAGTTGAAGATTTTGCACACAGTTCCTTCCAAATGGCTCTGTCTAAGGGTTGGCCTTTG
TATCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGGCGTTTTAAAGACATCTTTCAGGAGATATATGACAAGCA
GTACAAGTCCCAATTTGAAGCCCAAAAGATCTGGTATGAGCATAGGCTCATCGACGACATGGTGGCCCAAGCTATGAAAT
CAGAGGGAGGCTTCACCTGGGCCTGTAAAAACTATGATGATGACATGCAGTCAGACTCTGTGGCCCAAGGGTATGGCTCT
CTCGGCATGATGACCAGCGTGCTGGTTTGTCCAGATGGCAAGACAGTAGAAGCAGAGGCTGCCCATGGGACTGTAACCCG
TCACTACCGCATGTACCAGAAAGGACAGGAGATGTCCACCAATCCCATTGCTTCCATTTTTGCCTGGACCAGAGGGTTAG
CCCACAGAGCAAAGCTTGATAACAATAAAGAGCTTGCCTTCTTTGCAAATGCTTTGGAAGAAGTCTCTATTGAGACAATT
GAGGCTGGCTTCATGACCAAGGACTTGGCTGCTTGCATTAAAGGTTTACCCAATGTGCAACGTTCTGACTACTTGAATAC
GTTTGAGTTCATGGACAAACTTGGAGAAAACTTGCAGATCAAACTAGCTCAGGCCAAACTT

Alignment

ORF - retro_pabe_926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.2 %
• Parental protein coverage: 95.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATIT-PDEKRVEEFKLK
          IIWELIKEKLIFPY.ELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATIT..DEKRVEEFKLK
Retrocopy IIWELIKEKLIFPYMELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATIT<SDEKRVEEFKLK

Parental  QMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPS
          QMWKSPNGTIRNILGGTVFREAI.CKNIP.LVSGWVKPIIIG.HAYGDQYRATDFVVPGPGKVEI.YTPS
Retrocopy QMWKSPNGTIRNILGGTVFREAIFCKNIPWLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEISYTPS

Parental  DGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQE
          DGTQKVTYLVHNFEEGGGVAMGMYNQDKS.EDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQE
Retrocopy DGTQKVTYLVHNFEEGGGVAMGMYNQDKSVEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQE

Parental  IYDKQYKSQFEARKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPD
          IYDKQYKSQFEA.KIWYEHRLIDDMVAQAMKSEGGF.WACKNYD.D.QSDSVAQGYGSLGMMTSVLVCPD
Retrocopy IYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFTWACKNYDDDMQSDSVAQGYGSLGMMTSVLVCPD

Parental  GKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSVETIEA
          GKTVEAEAAHGTVTRHYRMYQKGQE.STNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVS.ETIEA
Retrocopy GKTVEAEAAHGTVTRHYRMYQKGQEMSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEA

Parental  GFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL
          GFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENL.IKLAQAKL
Retrocopy GFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLQIKLAQAKL

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	0.06 RPM	14.54 RPM
SRP007412_cerebellum	0.00 RPM	15.20 RPM
SRP007412_heart	0.03 RPM	34.41 RPM
SRP007412_kidney	0.23 RPM	172.33 RPM
SRP007412_liver	0.21 RPM	148.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_926 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_926 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_926 has 0 orthologous retrocopies within eutheria group .

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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,