RetrogeneDB ID: retro_bole_56

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C5:24492398..24492644(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo7g019910
• Aliases: None
• Description: None

Sequence

>retro_bole_56
ACTGATGTCTCATACCTGTGGCGTATGTGTAAGCTCAGATCTCCTCTCCATGGTTGTGTGTCTCCAACATGTCTGATGTC
ACCTTTTGTACTAGCCTCCCTCGGTTGGTAGCGTCGTCGACCGATGTCTGTCTGTGAATGTCGGTCGATTTATCGTTGCG
TCTGTCGATCGATGCTGATGCTTCTGGTCGACGCGCGATGTAACTCTGAATCTCCACTAATTCCCCTTGAATAGCTTCTA
TCTTGG

Alignment

ORF - retro_bole_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 65.08 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDVRML-ISVVAAEISCPWYCVSDMSDFTFGTNRPRFVASSTNVCLRMSVDMLLRLSIDADSSGRRCPEL
          TDV..L....V.A.IS.PW.CVS.MSD.TF.T..PR.VASST.VCL.MSVD..LRLSIDAD.SGRR...L
Retrocopy TDVSYL<VAYV*AQISSPWLCVSNMSDVTFCTSLPRLVASSTDVCL*MSVDLSLRLSIDADASGRRAM*L

Parental  YRS-LLPTDLSLLW
          ..S.L.P....L.W
Retrocopy *IS>LIPLE*LLSW

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_56 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo7g019910	2 retrocopies	retro_bole_56 , retro_bole_70,