RetrogeneDB ID: retro_btau_331

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:12034471..12035737(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.55792
• Ensembl ID: ENSBTAG00000030453
• Aliases: None
• Description: zinc finger CCCH domain-containing protein 14 isoform 1 [Source:RefSeq peptide;Acc:NP_001159774]

Sequence

>retro_btau_331
GATGAAGAACTTCCTGATTACATTATGGTGATAGTGACGAACAAGAAAAGTCAGGACCAAATGACAGAGGACCTGTCCCT
GTTTAAGGGAACAACACAATTTGACTCACTGTATGGCTTCATGGGGTATTATATAAACTTAGTTCTGTAACAACCGACCC
CTCTAGTCTGAAGTCTTCTGATACCAACCTCTTTGATGGTAACATACCTTCAAACAAGAGCAGTTTCAGTCGAGGAGATT
AGAGAAGGCACGAAGCTGCAGGGCCACCTCTTGCAGTTTCTAGCACTAGACCTGAAAAAAGAGAATCTAGAGTTTCTACA
AGTTCACAGGAGCAGAAAGCCACTAATGTCGGACAGATTTATAATAACGGAGCTGCAACCTGACCAATGTCAACAGTGAA
ACCTTTGAGGGAGCTAGCACCCTTTGAAGACGTGATTGATATTAAGCCAGAACCAGATGATCTCATTGATGAAGACCTCA
ATTTTGTGCAGGAGAAACCCTTATCTCAGAAAAAAACTACAGAGACACTTATATATGGTTCTTCTTGCCCTTCTATTGAA
ATTTATCGACCACCTGCAAGTCGAAAGCAGACAGTGGTGCTCATTTAAACAGGCTGCAATTTCAACAGCAGAAAAACAGT
ATTCATGCTGCCAAGCAACTTGATATTCAGAGTAGCCAGGTGTATGAAACAGGACGTTTGTGTGAACCAGAAGTGCTTAA
CAGCTTAGAAGAGACTTATGGTCCTTTCCTCAGGAACAACTCAGAAAAGATGAGTATTGAGGAAGAAAACTTTCAGAAGA
GAAAGTTGCCTGGGTAAGTTCAGTTGTTAAAGTAAAAAATTTCAGTCATGATGGAGAAGAGGAGGAGGAAGATGAGGATT
GTGGGTCCCCTACTGGAAGCATCTCCAGCAGTGTGTTAGTGCCAGCAAAACCTGAACGGAGACCCTCACTTCCACCTTCT
AAACAAGCTAACAAGAATCTAATTTTGAAGGCTCTATCCGAAGCTCAAGAATCTGTAACAAAAACAACTAACTATTCTAC
AGTCTCGCAGAAACGGACACTTTCAGTTGCTCCCAGAACTTGAACTCAAGAAGAATTGCTAGCAGAAATGGTCCAGGGAC
AAGGCAGCGTCCCCAGAATAAGCTCTCCCATTGAAGAGGAAGCAAAAGGAGATAATATATACAAAAGTCAAGGAACTCAA
CAGAGGCAGTTGTAACCCCTATTGCAAATTAAGCCCATGATGGCAGAAACTCTGCACATCAGTCGA

Alignment

ORF - retro_btau_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.58 %
• Parental protein coverage: 73.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DEELPDYIMVMVANKKSQDQMTEDLSLFLG-NNTIRFTVWLHGVLDKLRSVTTDPASLKSSDTNLFDGNV
          DEELPDYIMV.V.NKKSQDQMTEDLSLF.G.NNTI..TVWLHGVL.KL.SVTTDP.SLKSSDTNLFDGN.
Retrocopy DEELPDYIMVIVTNKKSQDQMTEDLSLFKG<NNTI*LTVWLHGVLYKLSSVTTDPSSLKSSDTNLFDGNI

Parental  PSNKSSFSRGDERRHEAAVPPLAVSSTRPEKRESRVSTSSQEQKATNVRQTYDDGAATRLMSTVKPLREL
          PSNKSSFSRGD.RRHEAA.PPLAVSSTRPEKRESRVSTSSQEQKATNV.Q.Y..GAAT..MSTVKPLREL
Retrocopy PSNKSSFSRGD*RRHEAAGPPLAVSSTRPEKRESRVSTSSQEQKATNVGQIYNNGAAT*PMSTVKPLREL

Parental  APSEDVIDIKPEPDDLIDEDLNFVQENPLSQKKTTVTLTYGSSRPSIEIYRPPATR-NTDSGAHLNRLQF
          AP.EDVIDIKPEPDDLIDEDLNFVQE.PLSQKKTT.TL.YGSS.PSIEIYRPPA.R...DSGAHLNRLQF
Retrocopy APFEDVIDIKPEPDDLIDEDLNFVQEKPLSQKKTTETLIYGSSCPSIEIYRPPASR<KADSGAHLNRLQF

Parental  QQQQNSIHAAKQLDIQSSRVYETGRLCEPEVLNSLEETYSPFFRSNAEKMSIEEENFRKRKLP-VVSSVV
          QQQ.NSIHAAKQLDIQSS.VYETGRLCEPEVLNSLEETY.PF.R.N.EKMSIEEENF.KRKLP..VSSVV
Retrocopy QQQKNSIHAAKQLDIQSSQVYETGRLCEPEVLNSLEETYGPFLRNNSEKMSIEEENFQKRKLP<WVSSVV

Parental  KVKKFSHDGEEEEEDDDCGSRTGSISSSVSVPAKPERRPSLPPSKQANKNLILKAISEAQESVTKTTNYS
          KVK.FSHDGEEEEED.DCGS.TGSISSSV.VPAKPERRPSLPPSKQANKNLILKA.SEAQESVTKTTNYS
Retrocopy KVKNFSHDGEEEEEDEDCGSPTGSISSSVLVPAKPERRPSLPPSKQANKNLILKALSEAQESVTKTTNYS

Parental  TVSQKQTLPVAPRTRTSQEDLLAEVAQGHGRVPRISSPVKEEEAQGGSVDERQGTQQRQLLSRLQIDPVM
          TVSQK.TL.VAPRT.T.QE.LLAE..QG.G.VPRISSP..EEEA.G......QGTQQRQL...LQI.P.M
Retrocopy TVSQKRTLSVAPRT*T-QEELLAEMVQGQGSVPRISSPI-EEEAKGDNIYKSQGTQQRQL*PLLQIKPMM

Parental  AETLQISQ
          AETL.IS.
Retrocopy AETLHISR

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	19.25 RPM
ERP005899_muscle	0.00 RPM	44.40 RPM
SRP017611_brain	0.00 RPM	72.17 RPM
SRP017611_kidney	0.00 RPM	58.20 RPM
SRP017611_liver	0.00 RPM	22.27 RPM
SRP030211_testis	0.01 RPM	410.88 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_331 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_331 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030453	1 retrocopy	retro_btau_331 ,
Callithrix jacchus	ENSCJAG00000017345	1 retrocopy	retro_cjac_1429,
Felis catus	ENSFCAG00000012898	1 retrocopy	retro_fcat_966,