RetrogeneDB ID: retro_btau_455

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:506961..507720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TALDO1
• Ensembl ID: ENSBTAG00000010336
• Aliases: None
• Description: transaldolase [Source:RefSeq peptide;Acc:NP_001030360]

Sequence

>retro_btau_455
GTGAAGCTGCAGAGGATGGATAGTGTGCTGGACCAGCTCAAACAGTTGATTGCAGTGGAGGCTGACACAGGCAATTTCCA
CCCTATTGACTAGTACGAGCCCCAGAATGCCAACACCAATGCATCATTGATCCTGGCCATGGCACAGATACCCATCTATC
AGGAGCCGGTGGAGGACGTCATAGCCTATGCAGGAGTCTCGGTGGGTAACAAGAGGAACAAATTATAAATGCTCTTGATA
AACTTTGTTTGCTATTTGGAGCAGAAATATTGAAGAAAATTCCAGGATGGGAATTCATGGAAGTGGATGCAAGGCTCTCT
TTCAATAAGAATGCCATGTTGGCCCAGCCCAGCACCCCATCAAGATATACAAAGAAGCCAGGATCATCAAGGACTGGATT
CTTATAAAACTGTCATCCACCTGAAAAAGAATTCAGTCTGGAAAGAAGCTAGAAGAGGAGCATGGCATGCACTACAGTAT
AACCCTACTCTTATCCTTTGCTCATGTGATGGGCTATGCAGAAACAGGTGAACTCATGTCCCCATTCCTGGGTTGTATTC
TCAACCAGCATGTGGCCAACACATACAAGAAGTTGTAGGAACCTCTGGAGGACTCACTAGTAAAGAGTGTCAACAAGATC
TGCAACTATTACAAGAAACTCCACTGTAAGATGATCATCATGGGTGCCTCCTTTCACAGCACTGCTATGTCAGGGCCTTG
GAAGCCTGGTGCTGTTTTCTCACCACCTCACCCCAGGTC

Alignment

ORF - retro_btau_455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.4 %
• Parental protein coverage: 75.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKRQRMENALDQLKQFTTVVADTGDFHAIDEYKPQDATTNPSLILAAAQMPTYQELVEEAIAYG-RKLGG
          VK.QRM...LDQLKQ...V.ADTG.FH.ID.Y.PQ.A.TN.SLILA.AQ.P.YQE.VE..IAY..R.LGG
Retrocopy VKLQRMDSVLDQLKQLIAVEADTGNFHPID*YEPQNANTNASLILAMAQIPIYQEPVEDVIAYA<RSLGG

Parental  SQEEQITNAIDKLFVLFGAEILKKIPGRVSTEVDARLSFDKDAMVAR-ARRLIELYKEAGISKERILIKL
          .QEEQI.NA.DKL..LFGAEILKKIPG....EVDARLSF.K.AM.A..A...I..YKEA.I.K..ILIKL
Retrocopy *QEEQIINALDKLCLLFGAEILKKIPGWEFMEVDARLSFNKNAMLAQ<AQHPIKIYKEARIIKDWILIKL

Parental  SSTWEGIQAGKELEEHHGIRCNMTLLFSFAQAVACAEAGVTLISPFVGRILDWHVANTDKKSYEPQEDPG
          SST...IQ.GK.LEE.HG.....TLL.SFA.....AE.G..L.SPF.G.IL..HVANT.KK..EP.ED..
Retrocopy SST*KRIQSGKKLEEEHGMHYSITLLLSFAHVMGYAETG-ELMSPFLGCILNQHVANTYKKL*EPLEDSL

Parental  VKSVTKIYNYYKKFGYKTIVMGASFRNTG-EIKAL-AGCDFLTISPQL
          VKSV.KI.NYYKK...K.I.MGASF..T.....AL.A.C.FLT.SPQ.
Retrocopy VKSVNKICNYYKKLHCKMIIMGASFHSTA<YVRALEAWCCFLTTSPQV

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	16.44 RPM
ERP005899_muscle	0.00 RPM	161.11 RPM
SRP017611_brain	0.00 RPM	38.46 RPM
SRP017611_kidney	0.00 RPM	66.09 RPM
SRP017611_liver	0.00 RPM	58.59 RPM
SRP030211_testis	0.01 RPM	47.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_455 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_455 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010336	1 retrocopy	retro_btau_455 ,
Macropus eugenii	ENSMEUG00000000841	1 retrocopy	retro_meug_756,
Mus musculus	ENSMUSG00000025503	2 retrocopies	retro_mmus_645, retro_mmus_667,
Rattus norvegicus	ENSRNOG00000018367	1 retrocopy	retro_rnor_2661,
Xenopus tropicalis	ENSXETG00000001671	1 retrocopy	retro_xtro_16,