RetrogeneDB ID: retro_bole_1

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C4:14957487..14958000(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo4g070470
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo2g096220
• Aliases: None
• Description: None

Sequence

>retro_bole_1
ATGGAGAAGAAGAAGAATAAAAGCGATGAATCAAAGCCGCCATTGATGGCGTTAAACCATGTATCAAGACTTTGCAGAGA
CGTCAAAAAGTCTCTCGAGTTCTACACGAAAGTGTTGGGGTTCGTGGAGACAGAGCGTCCCGCGTCCCTAGACTTCGACG
GTGCGTGGCTATTCAACTACGGTGTTGGGATCCATTTGGTGCAGGCTAAAGACGAAGAAAAGCTACCTTCAAACACGGAG
CATTTAGACCCAATGGATAACCACATCTCGTTCCAGTGCGAAGACATGGAAGCTTTGGAGAAGAGGCTCAAGGAAGTGGA
TGTGAAGTACATCAAGAGGACGGTAGGTGAGCAGGAAGACGCGGCTATCGACCAGCTCTTCTTTAATGATCCCGATGGTT
TCATGGTCGAGATTTGTAACTGCGAGAATCTTGAGCTTAAACCGCGTGATTCAGCTGATGCTATACGTCTCCCGGGAGAT
CGGCACGCGCCTCCTGTTTCTCTCCCTGGCTAG

Alignment

ORF - retro_bole_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.46 %
• Parental protein coverage: 79.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKSLNHISLLCRSVEESMNFYQHVLGFLPIRRPGSFDFDGAWLFGHGVGIHLLQSTEPEKLLKKTE-INP
          L..LNH.S.LCR.V..S..FY..VLGF....RP.S.DFDGAWLF..GVGIHL.Q....EKL...TE...P
Retrocopy LMALNHVSRLCRDVKKSLEFYTKVLGFVETERPASLDFDGAWLFNYGVGIHLVQAKDEEKLPSNTEHLDP

Parental  KDNHISFQCESMGAVEKKLNEMGIEYV-RAVVEEGGIQVDQLFFHDPDGFMIEICNCDSLPVVP
          .DNHISFQCE.M.A.EK.L.E....Y..R.V.E......DQLFF.DPDGFM.EICNC..L...P
Retrocopy MDNHISFQCEDMEALEKRLKEVDVKYIKRTVGEQEDAAIDQLFFNDPDGFMVEICNCENLELKP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brassica oleracea was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica oleracea was not studied using ChIP-Seq data.

EST

Brassica oleracea was not studied using EST data.

TSS

Brassica oleracea was not studied using FANTOM5 data.

Lab

retro_bole_1 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica oleracea does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G80160	1 retrocopy	retro_atha_15,
Brassica oleracea	Bo2g096220	1 retrocopy	retro_bole_1 ,
Brassica rapa	Bra008491	1 retrocopy	retro_brap_10,
Arabidopsis lyrata	fgenesh1_pm.C_scaffold_2001978	1 retrocopy	retro_alyr_14,
Medicago truncatula	MTR_2g103490	1 retrocopy	retro_mtru_44,
Setaria italica	Si023259m.g	1 retrocopy	retro_sita_39,