RetrogeneDB ID: retro_btau_723

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:49673198..49673759(-)
• Located in intron of: ENSBTAG00000002579

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGC152585
• Ensembl ID: ENSBTAG00000040368
• Aliases: None
• Description: alpha- and gamma-adaptin-binding protein p34 [Source:RefSeq peptide;Acc:NP_001092366]

Sequence

>retro_btau_723
GAGTGGTGTATCAAACATGGCTTTGAATTGGTAGAACTTAGTCCAGAAGAGTTGCCTGAGGAAGATGATGACCTCCCAGA
ATCTACAGGAGTAAATCAAATTGTTCAAGCCTTGAATGCCAATGTCTGGTCCAATGTAGTGATGAAGAATGAGAGGAACC
AAGGCCTTAACTGTCTCACCTCATTGACTGGCGCAAACCATAGCATTGGATCAACAGAGACCTGCCACTCAAAGCAGCCC
TGTGTTCCAGCAGCAGAGAGGACCAAATCCCTCTTGGATCATGGAGGGGCTGCCTCTAACACAGTAGACAGGCAGGTCGA
TAGCACTGTGGATCCCATGTTAGACCTGGATATTCGAGAACTTGCCAGTTTTACTACAGGTGGTGGAGATTTGGAGAATT
TTGAAAGACTGTTTTCAAAGTTAAAAGAAATGAAAGACAAGGCTGCGATGCTTCCTCATGAGCAAAGAAAGATGCATGCA
GAAAAGGTGGCCAAAGCCTTCTGGATGGCAACTGGGGGAGACAGAGATGAAATTGAAGGCATTTCATCTGAGGAAGAGCA
C

Alignment

ORF - retro_btau_723 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.3 %
• Parental protein coverage: 59.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EWCIKHGFELVELSPEELPEEDDDFPESTGVKRIVQALNANVWSNVVMKNERNQGLNLLSSLTGASHSIG
          EWCIKHGFELVELSPEELPEEDDD.PESTGV..IVQALNANVWSNVVMKNERNQGLN.L.SLTGA.HSIG
Retrocopy EWCIKHGFELVELSPEELPEEDDDLPESTGVNQIVQALNANVWSNVVMKNERNQGLNCLTSLTGANHSIG

Parental  SAESCHSEQPCVPAAERTESLLDHRGAASNTADVQVDSIVDPMLDLDIQELASLTTGGGDLENFERLFSK
          S.E.CHS.QPCVPAAERT.SLLDH.GAASNT.D.QVDS.VDPMLDLDI.ELAS.TTGGGDLENFERLFSK
Retrocopy STETCHSKQPCVPAAERTKSLLDHGGAASNTVDRQVDSTVDPMLDLDIRELASFTTGGGDLENFERLFSK

Parental  LKEMKDKAATLPHEQRKMHAEKVAKAFWMAIGGDRDEIEGLSSDEEH
          LKEMKDKAA.LPHEQRKMHAEKVAKAFWMA.GGDRDEIEG.SS.EEH
Retrocopy LKEMKDKAAMLPHEQRKMHAEKVAKAFWMATGGDRDEIEGISSEEEH

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	4.18 RPM
ERP005899_muscle	0.00 RPM	15.36 RPM
SRP017611_brain	0.00 RPM	32.43 RPM
SRP017611_kidney	0.00 RPM	33.01 RPM
SRP017611_liver	0.00 RPM	8.08 RPM
SRP030211_testis	0.02 RPM	23.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_723 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_723 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000040368	1 retrocopy	retro_btau_723 ,
Canis familiaris	ENSCAFG00000017414	1 retrocopy	retro_cfam_1891,
Monodelphis domestica	ENSMODG00000009585	1 retrocopy	retro_mdom_1416,
Rattus norvegicus	ENSRNOG00000008424	2 retrocopies	retro_rnor_1443, retro_rnor_2813,