RetrogeneDB ID: retro_btau_342

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:45164708..45165002(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AES
• Ensembl ID: ENSBTAG00000031363
• Aliases: None
• Description: amino-terminal enhancer of split [Source:RefSeq peptide;Acc:NP_001121969]

Sequence

>retro_btau_342
GAAATATCCTGCAGCTTTAACATCAAGATGCACAAGCAAGCTGAAATCTTCAAGGGGCTGAATGGGATAAGTGCCAGGAC
CCACCCTACCTTTCCCCAGAGCAGTAGCAGCAGTTCTTAGGAAACATCCAGTGGGCTAATAAGCAGGTTACAGTTCCTGA
GCTGAACTCCATCATCTGACAGAAACTACAAGCCCTCCAGCTTCCCAGCTGCAGGCTCTCGCCCTGCCCTGATCCCACTT
CCTGGGGAAGCTACAGCCCCTTCACTACTAGGACTTAGCACAGGCACTGGCCTC

Alignment

ORF - retro_btau_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.69 %
• Parental protein coverage: 52.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EMSYGLNIEMHKQAEIVKRLNGICA-QVLPYLSQEHQQQVLGAIERA-KQVTAPELNSIIRQQLQAHQL-
          E.S...NI.MHKQAEI.K.LNGI.A.Q..PYLS.E..QQ.LG.I..A.KQVT.PELNSII.Q.LQA.QL.
Retrocopy EISCSFNIKMHKQAEIFKGLNGISA<QDPPYLSPEQ*QQFLGNIQWANKQVTVPELNSII*QKLQALQL<

Parental  SQLQALALP-LTPLPVGLQPPSLPAVSAGTGL
          SQLQALALP.L.PLP.....PSL...S.GTGL
Retrocopy SQLQALALP<LIPLPGEATAPSLLGLSTGTGL

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	15.07 RPM
ERP005899_muscle	0.00 RPM	119.83 RPM
SRP017611_brain	0.00 RPM	143.89 RPM
SRP017611_kidney	0.00 RPM	84.94 RPM
SRP017611_liver	0.00 RPM	45.00 RPM
SRP030211_testis	0.00 RPM	46.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_342 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031363	1 retrocopy	retro_btau_342 ,
Otolemur garnettii	ENSOGAG00000016151	2 retrocopies	retro_ogar_1674, retro_ogar_2148,
Pongo abelii	ENSPPYG00000009364	2 retrocopies	retro_pabe_1812, retro_pabe_2155,