RetrogeneDB ID: retro_btau_259

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:55872820..55873456(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000033360
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PXMP4
• Ensembl ID: ENSBTAG00000038738
• Aliases: None
• Description: Peroxisomal membrane protein 4 [Source:UniProtKB/Swiss-Prot;Acc:A5PJL1]

Sequence

>retro_btau_259
ATGGTCGCCCCACCGCAGCTGCGGGCTCTGCTCTTTGCGATCAACGCACTATTGCGCAAGCGCCGCTACCACGCAGCACT
GGCCATGCTTAAGGGCTTCCGGAACGGGGCAGTCTATGGAGCCAAAATCCGGGCCCCTCACGCGCTGGTCATGACCTTTC
TTTTCCGGAGTGGCAGCCTCCGGGAGAAGCTGCGTGCCATCCTGCAGGCCACGTACACCCACTCCTGGAACCTAGCCAGG
TTTGTGTTCCTCTACAAGGGACTCTGTGCCCTGCAGTCCCACGTCCAGGGCAAGACCTACCAGGCACACTCATTCGTGTC
TGCCTTCATCGGGGGCTTGCTGGTGTTTGGAAACAACAATAACATCAACAGCCAGATCAGCATGTACCTGCTATCCCGCG
TCCTATTTGCCCTGTGCCGCCTGGGCGTGGAGAAGGGCTTCATCCCTGAACCCAGGTTGGACCCGTTTCCATGGTTCTCA
GGGCTGGTGTGGGGGCTGGTGCTGTGGCTCTTCGAGTACCACCGGCCAACCCTGCAGCCCTCGCTGCAGTCGTCCATGAC
CTACCTGTACGAGGACAGCAACGTGTGGCACGACCTCTCGGACTTCTTTATCTACAACAAGAGCCAACCCTCCAAG

Alignment

ORF - retro_btau_259 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVAPPQLRALLFAINALLSKRRYHAALAMLKGFRNGAVYGAKIRAPHALVMTFLFRSGSLREKLRAILQA
          MVAPPQLRALLFAINALL.KRRYHAALAMLKGFRNGAVYGAKIRAPHALVMTFLFRSGSLREKLRAILQA
Retrocopy MVAPPQLRALLFAINALLRKRRYHAALAMLKGFRNGAVYGAKIRAPHALVMTFLFRSGSLREKLRAILQA

Parental  TYTHSWNLARFVFLYKGLCALQSHVQGKTYQAHSFVSAFIGGLLVFGNNNNINSQISMYLLSRVLFALCR
          TYTHSWNLARFVFLYKGLCALQSHVQGKTYQAHSFVSAFIGGLLVFGNNNNINSQISMYLLSRVLFALCR
Retrocopy TYTHSWNLARFVFLYKGLCALQSHVQGKTYQAHSFVSAFIGGLLVFGNNNNINSQISMYLLSRVLFALCR

Parental  LGVEKGFIPEPRLDPFPWFSGLVWGLVLWLFEYHRPTLQPSLQSSMTYLYEDSNVWHDLSDFFIYNKSQP
          LGVEKGFIPEPRLDPFPWFSGLVWGLVLWLFEYHRPTLQPSLQSSMTYLYEDSNVWHDLSDFFIYNKSQP
Retrocopy LGVEKGFIPEPRLDPFPWFSGLVWGLVLWLFEYHRPTLQPSLQSSMTYLYEDSNVWHDLSDFFIYNKSQP

Parental  SK
          SK
Retrocopy SK

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	0.14 RPM
ERP005899_muscle	0.00 RPM	2.11 RPM
SRP017611_brain	0.00 RPM	0.27 RPM
SRP017611_kidney	0.00 RPM	0.71 RPM
SRP017611_liver	0.00 RPM	0.53 RPM
SRP030211_testis	0.03 RPM	0.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_259 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_259 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038738	2 retrocopies	retro_btau_1058, retro_btau_259 ,