RetrogeneDB ID: retro_btau_1712

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:85002558..85003296(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000037531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBXO25
• Ensembl ID: ENSBTAG00000007039
• Aliases: None
• Description: F-box only protein 25 [Source:UniProtKB/Swiss-Prot;Acc:Q1RMS8]

Sequence

>retro_btau_1712
GAAAACTGGATCTATGTCCATAAAGAAAGCACAAGAGAAAGACATGGCTACTGTACTTTGGGAGAAGCTTTTAATCGCTT
AGACTTCTCGAGTGCGATCCAGGACATCCGAAGGTTCAATTATGTGGTCAGGCTATTGCAGCTGATTGCAAAGTCCCAGC
TGACCTCGCTGAGTGGTGTGGCCCAGAAGAACTACTTCAACATCCTGGATAAGATCGTTCAGAAGGTTCTCGGTGACCAC
CAAAACCCTCGCCTGATCAAGGATCTTCTCCAAGACCTCAGCTCCACCCTGTGCATTCTGATCCGAGGAGTAGGGAAGTC
TGTGCTGGTGGGAAACATCAACATCTGGATTTGCCGATTAGAGACCGTTCTCCGCTGGCAGCAGCAGCTGCAGAATCTTC
AGATGACGGAGGTGGACAGTGGCCTGACGCTCAGCGACCTTCCTGTGCACATGCTCAGCAACATCCTGTACAGGTTCTCG
GATGGGTGGGACATCGTCACCCTGGGTCAGGTGACCCCGACACTGTCCGCGCTCAGCGAGGACCGGCAGCTGTGGAAGAA
GCTCTGCCAGTACCACTTTGGGGAGAAGCAGTTTTGTAGACACTTGATCCTTTCAGAAAAAGGCCATGTGGAGTGGAAGC
TGATGTATTTTGCACTTCAGAAGCACTACCCCACCAAGGAGCAGTATGGAGACACCCTGCACTTCTGCCGGCACTGCAGC
ATCCTCTTCTGGAAGGAC

Alignment

ORF - retro_btau_1712 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 68.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENWIYVHKESTRERHGYCTLGEAFNRLDFSSAIQDIRRFNYVVRLLQLIAKSQLTSLSGVAQKNYFNILD
          ENWIYVHKESTRERHGYCTLGEAFNRLDFSSAIQDIRRFNYVVRLLQLIAKSQLTSLSGVAQKNYFNILD
Retrocopy ENWIYVHKESTRERHGYCTLGEAFNRLDFSSAIQDIRRFNYVVRLLQLIAKSQLTSLSGVAQKNYFNILD

Parental  KIVQKVLGDHQNPRLIKDLLQDLSSTLCILIRGVGKSVLVGNINIWICRLETVLRWQQQLQNLQMTEVDS
          KIVQKVLGDHQNPRLIKDLLQDLSSTLCILIRGVGKSVLVGNINIWICRLETVLRWQQQLQNLQMTEVDS
Retrocopy KIVQKVLGDHQNPRLIKDLLQDLSSTLCILIRGVGKSVLVGNINIWICRLETVLRWQQQLQNLQMTEVDS

Parental  GLTLSDLPVHMLSNILYRFSDGWDIVTLGQVTPTLSALSEDRQLWKKLCQYHFGEKQFCRHLILSEKGHV
          GLTLSDLPVHMLSNILYRFSDGWDIVTLGQVTPTLSALSEDRQLWKKLCQYHFGEKQFCRHLILSEKGHV
Retrocopy GLTLSDLPVHMLSNILYRFSDGWDIVTLGQVTPTLSALSEDRQLWKKLCQYHFGEKQFCRHLILSEKGHV

Parental  EWKLMYFALQKHYPTKEQYGDTLHFCRHCSILFWKD
          EWKLMYFALQKHYPTKEQYGDTLHFCRHCSILFWKD
Retrocopy EWKLMYFALQKHYPTKEQYGDTLHFCRHCSILFWKD

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	15.00 RPM
ERP005899_muscle	0.11 RPM	17.31 RPM
SRP017611_brain	0.96 RPM	24.03 RPM
SRP017611_kidney	0.18 RPM	21.93 RPM
SRP017611_liver	0.08 RPM	6.19 RPM
SRP030211_testis	0.78 RPM	14.80 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1712 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1712 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007039	1 retrocopy	retro_btau_1712 ,
Cavia porcellus	ENSCPOG00000008110	1 retrocopy	retro_cpor_282,