RetrogeneDB ID: retro_ogar_1213

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873539.1:17681827..17682651(+)
• Located in intron of: ENSOGAG00000008191

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDK3
• Ensembl ID: ENSOGAG00000005598
• Aliases: None
• Description: pyruvate dehydrogenase kinase, isozyme 3 [Source:HGNC Symbol;Acc:8811]

Sequence

>retro_ogar_1213
TGGCTATTGAAGCAGCTGGCACCCAAGTAGACCAGGTGCTATTTGTGCCTCTTGTTGTAACTGGTCTCTGTTAAGCAGTT
CCTGGAATTTGGGAGAGATAATGATGTGAGAGTGCATCAGATATGATTCTACAGAAGGAGATTTTTGTGCTACTGTCTAA
CAATGTGAGGATGGTCAGTTTTTCTGCTGGATAATTTGCTTAACTGGCCTTCAGTGGGATTGGCTCAAAGCAGATATATA
CACAAATTTCTTGACCTTTTAGAATATGAACATAAGAGCTATGATGATCCACAGACCTTGAATAACTTTTCATAAGTCCT
GTTTAAAGTCATAAATAAAGCAATGATGTGGTCCCCACAGTGGTACATGGAATGATTAAATACAAAGAAAAATATGTGTT
TGATCCTTTATTAGTGATAATATCCCTATTTTCTGGATTGGTTTATACCAGCTGTATTTCTTCCCATATGCTTATTAGTC
AGCACACACTTTTGTTTCGTGGTGACACTATCTGGGCTCATCCTAAATACACAGGCACCATTGATCTCAGATGTAATATT
GCTGATGTTGTGAAAGATGTACATGCATATAGAACACCCAAGAGACTGTGTGAATGGTAATAACTGGTAGCTCCAGAGCT
GGAAACTGAAGAGTTTAATGACAAAGCTCCAGACAAACCTATTCAGATAGTTTATGTGCCTAGACATCTGTTTTACATGC
TATTCAAGAATTCGGTAAGAACAATAGTAGTACTACATGAAGACAGAAAGAAGAGATATTTGGCTATTGAAACCCTTGCT
ACTTTGGATAAAAAAGATTTATCC

Alignment

ORF - retro_ogar_1213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.4 %
• Parental protein coverage: 66.75 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  WLLKQPVPKQIERYSRFSPSPLSIKQFLDFGRDNA-CEKTSYMFLRKELPVRLANTMREVNL-LPDNLLN
          WLLKQ..PK....Y........S.KQFL.FGRDN..CE..S.M.L.KE..V.L.N..R.V...L.DNLLN
Retrocopy WLLKQLAPK*TRCYLCLLL*LVSVKQFLEFGRDND<CESASDMILQKEIFVLLSNNVRMVSF>LLDNLLN

Parental  RPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNFLQVLIKVRNR-HNDVVPTMAQGVIEYKEKFGFDP-
          .PSVGL.QS.Y...FL.LLEYE.KS..DPQ.L.NF..VL.KV.N...NDVVPT...G.I.YKEK..FDP.
Retrocopy WPSVGLAQSRYIHKFLDLLEYEHKSYDDPQTLNNFS*VLFKVINK<SNDVVPTVVHGMIKYKEKYVFDP<

Parental  FISSNIQ-YFLDRF-YTNRISFRMLINQHTLLFGGDTNPAHPKHIGSIDPTCNVADVVKD--AYETAKML
          FIS.NI..YFLD.F.YT..IS..MLI.QHTLLF.GDT..AHPK..G.ID..CN.ADVVKD..AY.T.K.L
Retrocopy FISDNIP<YFLDWF<YTSCISSHMLISQHTLLFRGDTIWAHPKYTGTIDLRCNIADVVKDVHAYRTPKRL

Parental  CEQYYLVAPELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYENRKEGYPAVKTLVTLG
          CE...LVAPELE.EEFN.KAPDKPIQ.VYVP.HLF.MLF...KNS.R..V.L.E.RK..Y.A..TL.TL.
Retrocopy CEW**LVAPELETEEFNDKAPDKPIQIVYVPRHLFYMLF---KNSVRTIVVLHEDRKKRYLAIETLATLD

Parental  KEDLS
          K.DLS
Retrocopy KKDLS

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_1213 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017832	1 retrocopy	retro_btau_911,
Erinaceus europaeus	ENSEEUG00000014090	2 retrocopies	retro_eeur_100, retro_eeur_690,
Otolemur garnettii	ENSOGAG00000005598	2 retrocopies	retro_ogar_1213 , retro_ogar_1980,
Otolemur garnettii	ENSOGAG00000014761	1 retrocopy	retro_ogar_509,