RetrogeneDB ID: retro_ogar_2925

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873682.1:347871..349104(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031767
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSOGAG00000014848
• Aliases: None
• Description: isocitrate dehydrogenase 1 (NADP+), soluble [Source:HGNC Symbol;Acc:5382]

Sequence

>retro_ogar_2925
ATGTCCATAACCATCAGTGGGGTTCCATGGAAGAAATGCAAGGAGTTGAAATGACATAAATCATTTGGGATTTGATAAAA
TAAAAACTCATTTTCCCTATGTGGAACTAGATCTACATAGCCACAATTTAGGCATAGAGAATCACGATGCCACCAGTGAC
CAAGTCACCAAGGATGCTACAGAGGCCATAAAGAATACAACATTGGGGTCATTGCTATTATCACCCCTAATGAGAAGAGG
GTTAAGAAGTCCAAGTTGAAACAAATGTGGAAATCACTGAATGGCACCATCCAAAATATCTTGGGTGGCACTGTCTTCAG
GGAAGCTAATGTCTGCTAAAATATCCCCAGGCTTGTGAGTGGACAGGTGAAACCCACCATCATAGGTCAACATGCTTTTG
GGGACCAATACAGAACAACCAATTTTGTTGTTCCCAGGCCTGGAAAAGTAGAGACAACTTATACATCAAGTGATAGAACC
CCAAAGGTGACATACATAGTGCATAACTTTGAAGGTGGTGGTGGTGTTGTAATGGGTATCTATAATCAAGCTAAGTCAAT
CCAAGATTTTGTGCATAGTTCCTTCCAAATGGCTCTGTATAACGGTTGGTCTTTGTATCTGAGTACTAAAAACACTATTC
TGAAGAAATATGAGGGATGTTTTAAAGAAATCTTTCAGGGGATATATGACAAGCAGTACAAATTCCAAGTTGAAGCCCAG
AAGATCTGGTATAAGCGTAGGTTCTTTGATGACATGTTGGCCCAAGCTATGAAATCAGAGGGAGGCTTCATCTGGGCCTG
CAAGCACTGTGATGGTGATGTGCAGTTGGACTCTGTGGCCCAAGGTTATGGCTCTCTTGGCATAATGACCAGTCTGTTGG
TTTGTCCAGATGGCAAGACAGTAGAAGAAGAGGCAGCCCATGGGACTGTAACCCACCACTACCATGTACCACAAAGGATA
GGAGACATCCACTAATCAAACTGCTCCATTTTGGCCTGGACCAGAGGGTTAGCCCATAGAGCAAAGCTTGATAACAATAA
AGAACTTGACTACTTGGCAAAGGCATTGGAAGAAGTCTGTATTGATACCATTGAGATTGACTTTATGACCAAGGACTTGG
CCATTTCCATTAAAGGTTTACCTAATGCACAATGTTCTGACTACCTGAATACATCCAAATTTATGGACAAACTTGGAGAA
AACTTGAAGATAAAACTAGCTCAGGCCAAATTG

Alignment

ORF - retro_ogar_2925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSKKISG-GSVVEMQGDEMTRIIWELIKEKLIFP-YVELDLHSYDLGIENRDATSDQVTKDAAEAIK-KY
          MS..ISG.GS..EMQG.EMT.IIW.LIK.KLIFP.YVELDLHS..LGIEN.DATSDQVTKDA.EAIK..Y
Retrocopy MSITISG<GSMEEMQGVEMT*IIWDLIK*KLIFP<YVELDLHSHNLGIENHDATSDQVTKDATEAIK<EY

Parental  NVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGD
          N.GV..A.ITP.EKRV...KLKQMWKS.NGTI.NILGGTVFREA..C.NIPRLVSG.VKP.IIG.HA.GD
Retrocopy NIGV-IAIITPNEKRVKKSKLKQMWKSLNGTIQNILGGTVFREANVC*NIPRLVSGQVKPTIIGQHAFGD

Parental  QYRATDFVVPGPGKVEITYTPNDGTQKVTYLVHNFEDGGGVAMGMYNQDKSIQDFAHSSFQMALSKSWPL
          QYR.T.FVVP.PGKVE.TYT..D.T.KVTY.VHNFE.GGGV.MG.YNQ.KSIQDF.HSSFQMAL...W.L
Retrocopy QYRTTNFVVPRPGKVETTYTSSDRTPKVTYIVHNFEGGGGVVMGIYNQAKSIQDFVHSSFQMALYNGWSL

Parental  YLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQ
          YLSTKNTILKKY.G.FK.IFQ.IYDKQYK.Q.EAQKIWY..R..DDM.AQAMKSEGGFIWACK..DGDVQ
Retrocopy YLSTKNTILKKYEGCFKEIFQGIYDKQYKFQVEAQKIWYKRRFFDDMLAQAMKSEGGFIWACKHCDGDVQ

Parental  SDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHY-RMYQKGQETSTNPIA-SIFAWTRGLAHRAK
          .DSVAQGYGSLG.MTS.LVCPDGKTVE.EAAHGTVT.H...MY.KG.ETSTN..A.SI.AWTRGLAHRAK
Retrocopy LDSVAQGYGSLGIMTSLLVCPDGKTVEEEAAHGTVT-HH>TMYHKG*ETSTNQTA<SILAWTRGLAHRAK

Parental  LDNNKELDLFAKALEEVCIETIEAGFMTKDLAICIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL
          LDNNKELD..AKALEEVCI.TIE..FMTKDLAI.IKGLPN.Q.SDYLNT..FMDKLGENLKIKLAQAKL
Retrocopy LDNNKELDYLAKALEEVCIDTIEIDFMTKDLAISIKGLPNAQCSDYLNTSKFMDKLGENLKIKLAQAKL

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2925 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 13 parental genes, and 20 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,
Otolemur garnettii	ENSOGAG00000034936	1 retrocopy	retro_ogar_334,
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,