RetrogeneDB ID: retro_btau_1731

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:17711701..17711884(+)
• Located in intron of: ENSBTAG00000020406

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.65336
• Ensembl ID: ENSBTAG00000038488
• Aliases: None
• Description: thymosin beta-4 [Source:RefSeq peptide;Acc:NP_001106702]

Sequence

>retro_btau_1731
ACAGCGCAGACCCGACTTCACTCGCTCGCAGTTCGCTTCGCACCCTCTGCAACCATGTCTGACAAACCCGATATGGCTGA
GATTAAGAAGTTCGATAAGTCGAAATTGAAGAAAATGGAAACGCAAGAGAAAAATCCACTGCCTTCGAAAGAAATGATTG
AAGAGAAGCAAGTAGGCGAGTCA

Alignment

ORF - retro_btau_1731 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAQIRLHSLAVRSAPSATMSDKPDMAEIEKFDKSKLKKTETQEKNPLPSKETIEQEKQAGES
          TAQ.RLHSLAVR.APSATMSDKPDMAEI.KFDKSKLKK.ETQEKNPLPSKE.IE.EKQ.GES
Retrocopy TAQTRLHSLAVRFAPSATMSDKPDMAEIKKFDKSKLKKMETQEKNPLPSKEMIE-EKQVGES

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	80.82 RPM
ERP005899_muscle	0.00 RPM	479.85 RPM
SRP017611_brain	0.00 RPM	161.66 RPM
SRP017611_kidney	0.00 RPM	226.77 RPM
SRP017611_liver	0.00 RPM	38.43 RPM
SRP030211_testis	0.02 RPM	163.41 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1731 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1731 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038488	2 retrocopies	retro_btau_1731 , retro_btau_599,
Gorilla gorilla	ENSGGOG00000006450	1 retrocopy	retro_ggor_200,
Macaca mulatta	ENSMMUG00000014256	2 retrocopies	retro_mmul_1274, retro_mmul_1890,
Pan troglodytes	ENSPTRG00000028317	4 retrocopies	retro_ptro_1440, retro_ptro_1572, retro_ptro_2864, retro_ptro_77,