RetrogeneDB ID: retro_btau_1044

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 24:32595644..32595932(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIMP
• Ensembl ID: ENSBTAG00000000640
• Aliases: VIMP, SELS
• Description: Selenoprotein S [Source:UniProtKB/Swiss-Prot;Acc:Q2KI76]

Sequence

>retro_btau_1044
AGAGGCCTCCTAAAGAATGAGGAGCTGTGTTTCCTTCACCTCACAGTGGGCTCCTTCCTGGGTACTCATGGATGGTAAAT
GTTTTCGGTTGTTGTGTCTTCTGTGTGATCTTTCAAAAGCTTTCCACCAAGTTGAGGGACGTAAGTCAGAGGCAACTAGA
CAGAGCTGTGGGAGCTATAAAACATGGTATCATTAAACAATAAGAAAGCTTTAGCAAGTACTCCTTTAGAAATGCAAAGG
GAATTAAATACACAAACTGAGAAGCATACAGAAAACTTATGGCAGCTT

Alignment

ORF - retro_btau_1044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.53 %
• Parental protein coverage: 51.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPTLETEGLRFLHVTVGSLLATYGWYI-VFSCILLYVVFQKLSTRLRALRQRHLDQAAAALEPDIVVKRQ
          R..L..E.L.FLH.TVGS.L.T.GW...VF.C....V.FQKLST.LR...QR.LD.A..A....I..K..
Retrocopy RGLLKNEELCFLHLTVGSFLGTHGW*M<VFGCCVFCVIFQKLSTKLRDVSQRQLDRAVGAIKHGI-IKQ*

Parental  EA-LAAARLKMQEELNAQVEKHKEKLRQL
          E..LA...L.MQ.ELN.Q.EKH.E.L.QL
Retrocopy ES>LASTPLEMQRELNTQTEKHTENLWQL

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	55.73 RPM
ERP005899_muscle	0.00 RPM	54.32 RPM
SRP017611_brain	0.00 RPM	21.56 RPM
SRP017611_kidney	0.00 RPM	33.19 RPM
SRP017611_liver	0.00 RPM	95.07 RPM
SRP030211_testis	0.00 RPM	121.14 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1044 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1044 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007115	1 retrocopy	retro_amel_177,
Bos taurus	ENSBTAG00000000640	1 retrocopy	retro_btau_1044 ,
Dasypus novemcinctus	ENSDNOG00000010694	2 retrocopies	retro_dnov_207, retro_dnov_880,
Echinops telfairi	ENSETEG00000011401	1 retrocopy	retro_etel_2096,
Felis catus	ENSFCAG00000028822	1 retrocopy	retro_fcat_1524,
Pteropus vampyrus	ENSPVAG00000012873	1 retrocopy	retro_pvam_1334,