RetrogeneDB ID: retro_btau_911

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:3536136..3537097(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000008357
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDK3
• Ensembl ID: ENSBTAG00000017832
• Aliases: None
• Description: [Source:RefSeq peptide;Acc:NP_001095404]

Sequence

>retro_btau_911
GGGAGAGAAAATGTGTGTGAGAAAACTTCATACATGTTCCTACAAAAGGAGCTTCCTGTGCGCCTGGCTAACACAATGCG
AGAAGTTAATCTTCTGCTGGAGGACTTGCTTAACAACCCTTCGGTGGAATTGGTTCAGAGCTGGTATATGCAGAGTTTTC
TTGAACTTCTAGAATATGAAAATCAGAGCCCTGAAGATCCACAGGTCTTGGATAACTTTCCACAAGTCCTAATTAAAGTC
AGAAATAAACACAATGATGTGGCTCCTACAATGGCCCAAGGAGTGATTGAGTACAAGGAGAAGTTTGGGTTTGATCCATT
CATTAGCAGTAACACCCAGTATTTTCTGGACCAATTTCATACCAACCACATCTCTTTCCACGTGCTTATTAACCAGCACA
CATTTCCATTTGGCAGTGACACCAACCCTGCACATCTGAGACACATCGGGAATATTGATCCCACCTGCAACGTCACTGGC
CTTGTGAAAGATGTGTATGAAACTGCCAAGATGCTTTGTGAGCTATATTATCTGGTAGCTCCAGAGCTGGAAGTTGAAGA
ATTCAGTGCCAAAGCTCCAAACAAATCTAATCAGGTAGTTTATGTGCCCTCACACCTCTTTCTCGTGCTGTTTGAGTTGT
TCAAGAACTCAATGAGAACAACAGTCGAACCATATGAAGAGAGAAAAGAGGGTACCCACTGTTAAAACCCTGGTTACTCT
GGTAAAGAAGACTTATCCACTAAGAGAGGTGACCTAGGTGGTGGGCTCCACTCTGAAAAATAGACTGCCGTTTTCACTAC
ACGTGTTCAACTACTCTGAGACCGAGCTGGAGCTTACCCAAGCCGCCCCGTCGGCTGGATTTGGTTGTGGCTTGCCAATT
TCTCGTCTGTATGCTAGATATTTCCAAGGAGATCTAAAACTCTATTCTATGGAAGGCGTGGTTACTGATGCTGTCATTTA
T

Alignment

ORF - retro_btau_911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 77.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GRDNACEKTSYMFLRKELPVRLANTMREVNLLPENLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVL
          GR.N.CEKTSYMFL.KELPVRLANTMREVNLL.E.LLN.PSV.LVQSWYMQSFLELLEYEN.SPEDPQVL
Retrocopy GRENVCEKTSYMFLQKELPVRLANTMREVNLLLEDLLNNPSVELVQSWYMQSFLELLEYENQSPEDPQVL

Parental  DNFLQVLIKVRNRHNDVVPTMAQGVIEYKEKFGFDPFISSNIQYFLDRFYTNRISFRMLINQHTLLFGGD
          DNF.QVLIKVRN.HNDV.PTMAQGVIEYKEKFGFDPFISSN.QYFLD.F.TN.ISF..LINQHT..FG.D
Retrocopy DNFPQVLIKVRNKHNDVAPTMAQGVIEYKEKFGFDPFISSNTQYFLDQFHTNHISFHVLINQHTFPFGSD

Parental  TNPVHPKHIGSIDPTCNVADVVKDAYETAKMLCEQYYLVAPELEVEEFNAKAPNKPIQVVYVPSHLFHML
          TNP.H..HIG.IDPTCNV...VKD.YETAKMLCE.YYLVAPELEVEEF.AKAPNK..QVVYVPSHLF..L
Retrocopy TNPAHLRHIGNIDPTCNVTGLVKDVYETAKMLCELYYLVAPELEVEEFSAKAPNKSNQVVYVPSHLFLVL

Parental  FELFKNSMRATVELYEDRKE-GYP-AVKTLVTL-GKEDLSIKISDLGGGV-PLRKIDRLFNYMYSTAPRP
          FELFKNSMR.TVE.YE.RKE.GYP..VKTLVTL.GKEDLS.K..DLGGG..PL.KID..F.Y..ST..RP
Retrocopy FELFKNSMRTTVEPYEERKE<GYP<TVKTLVTL<GKEDLSTKRGDLGGGL<PL*KIDCRFHYTCSTTLRP

Parental  S-LEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGVGTDAVIY
          S.LE.T.AAP.AGFG.GLPISRLYARYFQGDLKLYSMEGV.TDAVIY
Retrocopy S<LELTQAAPSAGFGCGLPISRLYARYFQGDLKLYSMEGVVTDAVIY

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
ERP005899_liver	0.00 RPM	7.86 RPM
ERP005899_muscle	0.00 RPM	36.90 RPM
SRP017611_brain	0.05 RPM	31.11 RPM
SRP017611_kidney	0.00 RPM	35.27 RPM
SRP017611_liver	0.00 RPM	4.45 RPM
SRP030211_testis	0.02 RPM	42.65 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_911 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_911 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 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,