RetrogeneDB ID: retro_ogar_334

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:31446664..31447871(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH2
• Ensembl ID: ENSOGAG00000034936
• Aliases: None
• Description: isocitrate dehydrogenase 2 (NADP+), mitochondrial [Source:HGNC Symbol;Acc:5383]

Sequence

>retro_ogar_334
GTGGTAGAGATGCAAGGAGATGAAATGACACGGATCATCTGGGAATTGATAAAAGAAAAACTCATTTTTCCCTATGTGGA
ACTGGATCTACATAGCTATGATTTAGGCATAGAGAATTGTGATGCCACCAGCAACCAAGTCACCAAGGATGCTGCAGAGG
CCATAAAAAAATACAACGTAGGGGTCAAGTGTGCTACTATCACCCCGATGAGAAGAGGGTTGAGTAGTTCAAGTTGAAAC
AAATGTGGAAATCACCGAACGGCACCATCCAAAATATTCTATGTGGCACTGTCTTCAGGGAAGCTATTATCTGCAAAAAT
ATCCCCCGGCTTGAGAGTGGATGGGTGAAACCCATCATCATAGGTCATCACGCTTATGGGGACCAATACAGAGCAACTGA
TTTTGTTGTTCCTGGGCCTGGAAAAGTAGAGATAACCTACACACCAAATGATGGAACCCAAAAGGTGACATACTTGGTAC
ATAACTTTGAAGATGGTGGTGGTGTTGCCATGGGTATGTACATTTAAGATAAGTCAATCCAAGATTTTGCACACAGTTCT
TTCCAAATGGCTCTGTCTAAGGGTTGACCTTTGTATCTGAGCACCAAAAGCACTATTCTGAAGAAATATGATGGACGTTT
TAAAGACATCTTTCAGGAGATATATGACAAGCAGTACAAATCCCAATTTGAAGCCCAGAAGATCTGGTATGAACATAGGC
TCATCGATGACACGGTGGCCCAAGCCACCAGAAATCAGAAGGAAGCTTCATTTGGGCCTGCAAAAACTATGATGGTGACG
TGCAGTCGGACTCTGTGGCCCAAGGTTATGGTTCTCTTGGCATGATGACCAGTGTGCTGGTTTGTCCAGATGGCAAAACA
GTAGAAGCAGAGGCAGCCCATGGGACCGTAACCCATCACAACCGCATGTACCAGAAAGGACAGGAGACATCCACTCATCC
CATTGCTTCCATTTCTGCCTGGACCAGAGGATTAGCCCACAGAGCAAAGCTTGATAACAATAAAGAACTTGACCTCTTTG
CAAAGGCTTTGGAAGAAGTCTGTATTGAGACCATTGAGGCTGGCTTCATGACCAAGGACTTGGCTATTTGCATTAAAGGT
TTACCTAACGTGCAACGTTCTGACTACTTGAATACATTTGAATTCATGGACAAACTTGGAGAAAACTTGAAGATAAAGCT
GGCCCAG

Alignment

ORF - retro_ogar_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.76 %
• Parental protein coverage: 88.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVEMDGDEMTRIIWQFIKEKLILPHVDVQLKYFDLGLPNRDQTNDQVTIDSALATQKYHVAVKCATITP-
          VVEM.GDEMTRIIW..IKEKLI.P.V...L...DLG..N.D.T..QVT.D.A.A..KY.V.VKCATITP.
Retrocopy VVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENCDATSNQVTKDAAEAIKKYNVGVKCATITP<

Parental  DEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVADR
          DE.RVE.FKLK.MWKSPNGTI.NIL.GTVFRE.IICKNIPRL..GW.KPI.IG.HA.GDQY.ATDFV...
Retrocopy DEKRVE*FKLKQMWKSPNGTIQNILCGTVFREAIICKNIPRLESGWVKPIIIGHHAYGDQYRATDFVVPG

Parental  AGTFKMVFTPKDGSGVKEWEVYNF-PAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKA
          .G......TP.DG.......V.NF...GGV.MGMY..D.SI..FAHS.FQ.A..K..PLY.STK.TILK.
Retrocopy PGKVEITYTPNDGTQKVTYLVHNFEDGGGVAMGMYI*DKSIQDFAHSSFQMALSKG*PLYLSTKSTILKK

Parental  YDGRFKDIFQEIFDKHYKTDFDKNKIWYEHRLIDDMVAQVLKS-SGG-FVWACKNYDGDVQSDILAQGFG
          YDGRFKDIFQEI.DK.YK..F...KIWYEHRLIDD.VAQ.....S.G.F.WACKNYDGDVQSD..AQG.G
Retrocopy YDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDTVAQATRN<SEGSFIWACKNYDGDVQSDSVAQGYG

Parental  SLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFA
          SLG.MTSVLVCPDGKT.EAEAAHGTVT.H.R..QKG..TST.PIASI.AWTRGL.HR.KLD.N..L..FA
Retrocopy SLGMMTSVLVCPDGKTVEAEAAHGTVTHHNRMYQKGQETSTHPIASISAWTRGLAHRAKLDNNKELDLFA

Parental  QTLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTSDFLDTIKANLDSALGR
          ..LE.VC.ET.E.G.MTKDLA.CI.GL.NV......LNT..F.D....NL...L..
Retrocopy KALEEVCIETIEAGFMTKDLAICIKGLPNVQRSD-YLNTFEFMDKLGENLKIKLAQ

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_334 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000010171	1 retrocopy	retro_lafr_176,
Macropus eugenii	ENSMEUG00000009797	1 retrocopy	retro_meug_124,
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 ,