RetrogeneDB ID: retro_ogar_1980

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873578.1:7348000..7349245(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029008
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1980
ATGCGGCTGTTCCGGCGGCTGCTGAAGCCGCCGGTGCCCGAGCAGATCGAGCACTACTCGCGCTTTTCGCCGTCGCCGCT
CTCCATCAAACAGTTCCTGGACTTCGGGAGAGACAACGCATGTGAGAAAACTTCTTATATGTTTCTACGAAAGGAGCTTC
CGGTACGCCTGGCTAACACCATGAGAGAAGTTAATCTTCTGCCGGATAATTTACTTAACCGCCCTTCAGTGGGACTGGTT
AAGAGTTGGTATATGCAGAGCTTTCTGGAACTCCTAGAATATGAAAATAAGAGCCCTGAGGATCCACGGGTCTTGGATAA
CTTTCTACAAGTTCTGATCAAAGTCAGAAATAGGCACAATGATGTGGTTCCTACAATGGCACAAGGAGTGATTGAATACA
AGGAGAAGTTTGGATTCGATCCTTTCGTTAACAGTAACATTCAGTATTTTCTGGATCGATTTTACACCAACCGCATCTCT
TTCCGCATGCTTATCAACCAGCACACACTTCTGTTTGGTGGTGACACTAATCCTGCTCATCCTAAACACATAGGGAGTAT
TGATCCTACCTGTAACGTGGCTGACGTGGTGAAAGATGCCTATGAAACAGCCAAGATGCTATGTGAACAGTACTACCTGG
TAGCTCCAGATCTGGAAGTCGAAGAATTCAATGCCAAAGCGCCAGACAAACCTATTCAGGTAGTTTATGTGCCCTCACAT
CTGTTTCACATGCTATTTGAGTTGTTCAAGAACTCAATGAGAGCAACGGTGGAACTCCATGAAGATAGAAAAGAAGGCTA
CCCGGCTGTTAAAACCCTTGTTACCCTGGGGAAAGAAGACTTATCCATTAAGATAAGTGACCTAGGTGGTGGTGTCCCAC
TCCGAAAAATAGATCGTCTTTTTAACTACATGTATTCAACTGCTCCTAGACCTAGCCTGGAGCCTACAAGAGCTGCCCCT
TTGGCTGGATTTGGTTACGGCTTGCCAATTTCTCGTCTGTATGCTAGATATTTTCAGGGAGATTTGAAACTGTATTCCAT
GGAAGGAGTGGGTACTGATGCTGTCATTTATTTGAAGGCTCTTTCAAGTGAATCATTTGAGAGACTTCCAGTTTTTAATA
AGTCTGCATGGCGTCATTACAAGACCACTCCTGAAGCTGACGATTGGAGCAATCCCAGCAAGGAACCTAAGGACGCTTCA
AAATATAAAGCTAAACAGGACAAGATCCAGACTAATAGAACTTTG

Alignment

ORF - retro_ogar_1980 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLFRWLLKQPVPKQIERYSRFSPSPLSIKQFLDFGRDNACEKTSYMFLRKELPVRLANTMREVNLLPDN
          MRLFR.LLK.PVP.QIE.YSRFSPSPLSIKQFLDFGRDNACEKTSYMFLRKELPVRLANTMREVNLLPDN
Retrocopy MRLFRRLLKPPVPEQIEHYSRFSPSPLSIKQFLDFGRDNACEKTSYMFLRKELPVRLANTMREVNLLPDN

Parental  LLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNFLQVLIKVRNRHNDVVPTMAQGVIEYKEKFGFD
          LLNRPSVGLV.SWYMQSFLELLEYENKSPEDP.VLDNFLQVLIKVRNRHNDVVPTMAQGVIEYKEKFGFD
Retrocopy LLNRPSVGLVKSWYMQSFLELLEYENKSPEDPRVLDNFLQVLIKVRNRHNDVVPTMAQGVIEYKEKFGFD

Parental  PFISSNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNPAHPKHIGSIDPTCNVADVVKDAYETAKMLCEQ
          PF..SNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNPAHPKHIGSIDPTCNVADVVKDAYETAKMLCEQ
Retrocopy PFVNSNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNPAHPKHIGSIDPTCNVADVVKDAYETAKMLCEQ

Parental  YYLVAPELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYENRKEGYPAVKTLVTLGKED
          YYLVAP.LEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVEL.E.RKEGYPAVKTLVTLGKED
Retrocopy YYLVAPDLEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELHEDRKEGYPAVKTLVTLGKED

Parental  LSIKISDLGGGVPLRKIDRLFNYMYSTAPRPSLEPSRAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGV
          LSIKISDLGGGVPLRKIDRLFNYMYSTAPRPSLEP.RAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGV
Retrocopy LSIKISDLGGGVPLRKIDRLFNYMYSTAPRPSLEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGV

Parental  GTDAVIYLKALSSESFERLPVFNKSAWRHYKTTPEADDWSNPSREPKDASKYKAKLDKIQTNRTL
          GTDAVIYLKALSSESFERLPVFNKSAWRHYKTTPEADDWSNPS.EPKDASKYKAK.DKIQTNRTL
Retrocopy GTDAVIYLKALSSESFERLPVFNKSAWRHYKTTPEADDWSNPSKEPKDASKYKAKQDKIQTNRTL

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_1980 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.

---

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,