RetrogeneDB ID: retro_btau_547

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:56854032..56854417(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B3
• Ensembl ID: ENSBTAG00000019787
• Aliases: None
• Description: Platelet-activating factor acetylhydrolase IB subunit gamma [Source:UniProtKB/Swiss-Prot;Acc:Q29460]

Sequence

>retro_btau_547
GTAGCCGATAGCAAAGATGAGGAACCTTAAGTCTTCATCAGGGACTCCTTGGTCCAGCTCAGGGACCAGTGGGGAAATCT
GGCAGGAGCTCTTTTCCCCTCTGCACGCACTTACCTTTGGCATTGGCTGTGACAGCACGCAGCATGGGCTGTGGAATTGG
GAGAATGAGAACACAGAGCTGGAACACCTCCGCCCCTAGACGGCGGTGGTCTGGGTAGGTACCAACAACCATGGGCGCAC
CACAGAGCAGGTAGGTGGCTGGTGGCATCAAGGCCATAGTGCAACTGGTGAACGCAGCGGCAGCCCCAGGTATGGGCTCA
CGGTACTCCGCCTGCTTATCTGGGGCCAGGGTCCCAACCCACTTCCAGAGAAAAACCGACAGGTG

Alignment

ORF - retro_btau_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.08 %
• Parental protein coverage: 53.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VADSKDKEPEVVFIGDSLVQLMHQC-EIWRELFSPLHALNFGIGGDSTQHVLWRL--ENGELEHIRPKIV
          VADSKD.EP.V.FI.DSLVQL..Q..EIW.ELFSPLHAL.FGIG.DSTQH.LW....EN.ELEH.RP...
Retrocopy VADSKDEEP*V-FIRDSLVQLRDQW>EIWQELFSPLHALTFGIGCDSTQHGLWNWENENTELEHLRP*TA

Parental  VVWVGTNNHGHTAEQVTGGIKAIVQLVNER--QPQARVVVLGLLPRGQHPNPLREKNRRV
          VVWVGTNNHG.T.EQV.G..........ER...P.....VL.LL..GQ.PNPL.EKNR.V
Retrocopy VVWVGTNNHGRTTEQVGGWWHQGHSATGERSGSPRYGLTVLRLLIWGQGPNPLPEKNRQV

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	0.58 RPM
ERP005899_muscle	0.00 RPM	21.12 RPM
SRP017611_brain	0.00 RPM	11.10 RPM
SRP017611_kidney	0.00 RPM	16.48 RPM
SRP017611_liver	0.00 RPM	0.45 RPM
SRP030211_testis	0.00 RPM	8.28 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_547 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019787	1 retrocopy	retro_btau_547 ,
Canis familiaris	ENSCAFG00000004847	1 retrocopy	retro_cfam_610,
Dasypus novemcinctus	ENSDNOG00000002870	1 retrocopy	retro_dnov_1276,
Macaca mulatta	ENSMMUG00000012172	1 retrocopy	retro_mmul_18,
Mustela putorius furo	ENSMPUG00000007574	1 retrocopy	retro_mputfur_351,
Rattus norvegicus	ENSRNOG00000020481	1 retrocopy	retro_rnor_976,