RetrogeneDB ID: retro_btau_1114

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:20915896..20916209(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000033021
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.87823
• Ensembl ID: ENSBTAG00000007586
• Aliases: None
• Description: synaptojanin-2-binding protein [Source:RefSeq peptide;Acc:NP_001030432]

Sequence

>retro_btau_1114
AACAGAAGAACAGATTACTTGGTTACTGAGGAAGAGATCAGTCTCACTAGAGGACCATCAGGCCTGGGCTTCAACATCAT
CGGTGGGACAGATCAGCAGTATGTCTCCAATGACAGTGGCATCTTCGTCAGCCGCGTCAAAGAGAATAGGGCTGTGGGCT
CTGGATGGGTGGCTCCAGGAGGGTGATAAGATCTGCTTGGTCAATGGCCAAGACCTAAAGAATCTGCTGCACCAGGATGC
CGTAGACCTTTTCTGTAATGCAGGCTATGCTGTGTCCCTGAGAGTGCAGCACAGGTTACAGGTGCAGAATGGG

Alignment

ORF - retro_btau_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 71.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGRVDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIFVSRIKENGAA-ALDGRLQEGDKILSVNG
          N.R.DYLVTEEEI.LTRGPSGLGFNI.GGTDQQYVSNDSGIFVSR.KEN.A..ALDG.LQEGDKI..VNG
Retrocopy NRRTDYLVTEEEISLTRGPSGLGFNIIGGTDQQYVSNDSGIFVSRVKENRAV>ALDGWLQEGDKICLVNG

Parental  QDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQNG
          QDLKNLLHQDAVDLF.NAGYAVSLRVQHRLQVQNG
Retrocopy QDLKNLLHQDAVDLFCNAGYAVSLRVQHRLQVQNG

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	0.07 RPM	8.15 RPM
ERP005899_muscle	0.16 RPM	13.78 RPM
SRP017611_brain	0.05 RPM	10.10 RPM
SRP017611_kidney	0.00 RPM	19.14 RPM
SRP017611_liver	0.00 RPM	9.67 RPM
SRP030211_testis	0.15 RPM	12.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1114 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007586	1 retrocopy	retro_btau_1114 ,
Cavia porcellus	ENSCPOG00000023967	1 retrocopy	retro_cpor_836,
Dipodomys ordii	ENSDORG00000010450	1 retrocopy	retro_dord_443,
Gorilla gorilla	ENSGGOG00000014492	1 retrocopy	retro_ggor_1470,
Macaca mulatta	ENSMMUG00000011086	1 retrocopy	retro_mmul_2308,
Mus musculus	ENSMUSG00000090935	3 retrocopies	retro_mmus_1428, retro_mmus_1538, retro_mmus_1802,
Oryctolagus cuniculus	ENSOCUG00000008559	1 retrocopy	retro_ocun_885,
Otolemur garnettii	ENSOGAG00000013211	1 retrocopy	retro_ogar_1515,