RetrogeneDB ID: retro_btau_866

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:43575730..43577277(-)
• Located in intron of: ENSBTAG00000001435

Retrocopy information

• Ensembl ID: ENSBTAG00000047365
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UPF3A
• Ensembl ID: ENSBTAG00000020858
• Aliases: None
• Description: None

Sequence

>retro_btau_866
ATGCGCTCGGAGGATGGAGCCGGGGGCCCCGGTGTGGCCGTTGCTACACGGGGTCCGAGCGGGAGGGAGAAACCATCACC
CGCAGAAAGCCAGCTCCGCCGGGAGTCTCCGCGGCGGGAGGCCGAAGCGCCGCTGGCCTCCTCTTCCAGCTGTGGGAGCG
GCGCAGGCAAACCTCGCGAGGAAAAGAGGACGGTCTTGAGCAAAGTGGTCATCCGGCGGCTTCCGCCCAGCCTCACCAAG
GAGCAGCTGGAACAGCAGCTGCACCCGCTGCCTGCACACGATTACTTCGAGTTCTTTACTGCTGATGTCAGTCTTTATCC
TCATCTCTACTCAAGAGCATACATTAACTTTAGAAATCCAGATGACATCCTTCTTTTTAGAGATCGTTTTGATGGATATA
TCTTCATTGATAATAAAGGGCTAGAATATCCTGCAGTGGTAGAATTTGCTCCATTCCAGAAGATAGCCAAAAAGAAGCTA
AAGAAAAAAGATGCCAAAACCGGAAGCATTGAAGATGACCCAGAGTATAAGAAATTTTTAGAAACTTACTGTGTGGAGGA
GGAGAAAACTAGTGTCAGTCCTGAAACTCTTCTGGGAGACATAGAGGCAAAGACACGAGAACTTATTGCTAGAAGAACCA
CACCTCTCTTGGAATATATTAAGAACAGAAAATTAGAGAAGCAGCTAATTCGAGAAGAAAAACGAGAGGAGCGGAGGAGG
AGGGAGCTGGAAAAGAAGCGCCTACGGGAAGAAGAGAAGCGGAGGCGAAGCCGAGGCGGCGGGAGGAGGAGAAGTGCAGG
AGGAAAGCAGCAGAAAAACAGAAGAAAACGGCGGAGAAGGAAGTAAGGATGAAGCTTCTCAAAAAACCAGAAAAGGGAGA
GGAGCCGAGCACTGAGAAACCAAAAGAAAGAGCGGAGGAGACTGACCCTGGAGACGGGAAGTGGGAGCCCTGTCCCAGTG
CGGTGGTCCTGAAGCCCAAGCCCCCAGAGGGCTCGCTGGAGGAGCTCCGGGAGAGGTCACAATATGACAGTGATAAAGAG
CAAAGGGATAAGGAGAGAAGATCCCGAGAAAAAGAACTTGAAGCACAGCAATGCCACTTGGATGACAGCAGGAAACACAG
AGCCCACCATGAGCTGGAAAAATGTTCGGGAAGAAATGGAGAAGAGCTGGCACGGGGGAAGGGGTCGGCCGCAGACGGAG
GGAGAAGAGGGAGCCGGGATAGGGGCTGCCCTGTGGAAGCAGCAGAGAGGCTGGGAAAGGAGAAGAGTGAAGACTAGCCG
GCACCCAGAAAGGAGCACACGGGAAACAAGGACCGGCCAGGCTTGCAGCTGTACCAGCCCAGAGCTCGCATCCGAGCCTG
TGACTGTGATGGAAGACACCCTGAGGAGGGCCGCGACGGGAGGAGGGGTGAGGCGGAAGACTCAACGGTGGCTTTAGCTG
AGAAGAGCGAAGAGGCGGTGTGGGGCGACAAGCATGTTGGTGACGTGGGTGGGGGCTCCCCACCTCAACGCTCTGTGGAT
TCGAGAGGGCGTTCCTTCCGGAAGTTA

Alignment

ORF - retro_btau_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRSEDGAGGPGVAVATRGPSGREKPSSAESQFRRESPRREAEAPLASSSSCGSGAGKPREEKRTVLSKVV
          MRSEDGAGGPGVAVATRGPSGREKPS.AESQ.RRESPRREAEAPLASSSSCGSGAGKPREEKRTVLSKVV
Retrocopy MRSEDGAGGPGVAVATRGPSGREKPSPAESQLRRESPRREAEAPLASSSSCGSGAGKPREEKRTVLSKVV

Parental  IRRLPPSLTKEQLEQQLHPLPAHDYFEFFTADVSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFIDSKV
          IRRLPPSLTKEQLEQQLHPLPAHDYFEFFTADVSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFID.K.
Retrocopy IRRLPPSLTKEQLEQQLHPLPAHDYFEFFTADVSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFIDNK-

Parental  KGLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYKKFLETYCVEEEKTSVSPETLLGDIEAKTREL
          .GLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYKKFLETYCVEEEKTSVSPETLLGDIEAKTREL
Retrocopy -GLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYKKFLETYCVEEEKTSVSPETLLGDIEAKTREL

Parental  IARRTTPLLEYIKNRKLEKQRI----REEKR-EERRRRELEKKRLREEEKRRRREEEKCRRKAAEKQKKT
          IARRTTPLLEYIKNRKLEKQ.I....REE.R.EE....E....R...E.K.RRREEEKCRRKAAEKQKKT
Retrocopy IARRTTPLLEYIKNRKLEKQLIREEKREERR<EEGAGKEAPTGRREAEAKPRRREEEKCRRKAAEKQKKT

Parental  AEKE----LLKKPEKGEEPSTEKPKERAEETDPGDGKWEPCPSAVVLKPKPPEGSLEELRERSQNDSDKE
          AEKE....LLKKPEKGEEPSTEKPKERAEETDPGDGKWEPCPSAVVLKPKPPEGSLEELRERSQ.DSDKE
Retrocopy AEKEVRMKLLKKPEKGEEPSTEKPKERAEETDPGDGKWEPCPSAVVLKPKPPEGSLEELRERSQYDSDKE

Parental  QRDKERRSREKELEAQQCHLDDSRKHRAHHELEKCSGRNGEELARGKGSAADGGRRGSQDRGCPVEAAER
          QRDKERRSREKELEAQQCHLDDSRKHRAHHELEKCSGRNGEELARGKGSAADGGRRGS.DRGCPVEAAER
Retrocopy QRDKERRSREKELEAQQCHLDDSRKHRAHHELEKCSGRNGEELARGKGSAADGGRRGSRDRGCPVEAAER

Parental  PGRENSEDRLAPRKERTGNKDRPGLQLYQPRARIRACDCDGRHPEEARDGRRGEAEDSTVALAEKSEEAV
          .G.E.SED..APRKE.TGNKDRPGLQLYQPRARIRACDCDGRHPEE.RDGRRGEAEDSTVALAEKSEEAV
Retrocopy LGKEKSED*PAPRKEHTGNKDRPGLQLYQPRARIRACDCDGRHPEEGRDGRRGEAEDSTVALAEKSEEAV

Parental  WGDMHVGDVGGGSPPQRSVDSRGRSFRKL
          WGD.HVGDVGGGSPPQRSVDSRGRSFRKL
Retrocopy WGDKHVGDVGGGSPPQRSVDSRGRSFRKL

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	1.51 RPM	2.52 RPM
ERP005899_muscle	1.43 RPM	2.69 RPM
SRP017611_brain	5.39 RPM	40.24 RPM
SRP017611_kidney	2.37 RPM	4.33 RPM
SRP017611_liver	0.83 RPM	2.94 RPM
SRP030211_testis	12.98 RPM	135.55 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_866 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_866 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020858	1 retrocopy	retro_btau_866 ,
Pan troglodytes	ENSPTRG00000006073	1 retrocopy	retro_ptro_1177,