RetrogeneDB ID: retro_bole_39

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C1:23022864..23023080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo1g024160
• Aliases: None
• Description: None

Sequence

>retro_bole_39
AGGTTCACATCAGGGGGAGTAGTGCGTGTTGTACTCTTTTTCCTTCATCATGGTTTTGTCCCACTGGGTTTTCCTGATAA
GCTTTTAATGAGGCAACATGAAGCGTATTACAGATCCTGTATGGTTATGGCATCCAAGGGGGAGTGTTATAAATCATGGA
GTGGATTGTCATTAACCAAGACAAGAGAAGAAAGCCCGTCAGCCACATCAAGCCCA

Alignment

ORF - retro_bole_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.7 %
• Parental protein coverage: 58.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSTSGGVVRVVLFFLHHGFVPLGFPDKLADVVKHFSAKYGKDFVSAAVG--LQSDSGVSRLLVDKLSVKA
          R.TSGGVVRVVLFFLHHGFVPLGFPDKL........A.Y....V.A..G....S.SG.S.......S..A
Retrocopy RFTSGGVVRVVLFFLHHGFVPLGFPDKL--LMRQHEAYYRSCMVMASKGECYKSWSGLSLTKTREESPSA

Parental  PDGP
          ...P
Retrocopy TSSP

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_39 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo1g024160	3 retrocopies	retro_bole_39 , retro_bole_65, retro_bole_69,