RetrogeneDB ID: retro_bole_47

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C3:25334960..25335362(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo4g127370
• Aliases: None
• Description: None

Sequence

>retro_bole_47
GGTAGAATTAGATATGACTTAGAGCTGTGCATGTTCTGTTTATTTACAGTGAAGAAAGCTTTTATTAAAATTGTTTTCTG
TTATGTTCAACAGAATGCTAAGGGTAAGAGGGGGCATGTTTATGGACTCGGCAGTGCCCAATACAGGGACAAATCACCTT
CTTCACGCGTCCCTAATGGTCTTGTCTGCAACCTGGAGCTGGAGATGCGTGTGGGAGGTCTTGAGACAAGCCTCCAAAGT
GTGAGGGAGGGTGTGTTTGAGGTGAAGCAGGATGTGTCCGAGATGACGCAGGACTTTGCATCAACAAGAGATGCAATCAA
TCAGCTGCTCCAAACGCTTCGTCCCCCACAAGCACCTACTGAACAGACTTCTGCTCAGCCCCAAGCCCAAACTCCTCAGC
CT

Alignment

ORF - retro_bole_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.45 %
• Parental protein coverage: 50.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRAKRLQNLASLILWLRLLVLVLTVFPFPSQNAKGKRGHVYGLGSAQYREYTPSSRVPNGLARNLELEMR
          GR......L....L..........VF....QNAKGKRGHVYGLGSAQYR...PSSRVPNGL..NLELEMR
Retrocopy GRIRYDLELCMFCLFTVKKAFIKIVFCYVQQNAKGKRGHVYGLGSAQYRDKSPSSRVPNGLVCNLELEMR

Parental  VGGLETSLQSVTADIAEVKQDVSEMKQDFAATRDGINQLLQTLRPQQAPTGQTSAQPQAPTTQP
          VGGLETSLQS..................FA.TRD.INQLLQTLRP.QAPT.QTSAQPQA.T.QP
Retrocopy VGGLETSLQSXXXXXXXXXXXXXXXXXXFASTRDAINQLLQTLRPPQAPTEQTSAQPQAQTPQP

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_47 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo4g127370	1 retrocopy	retro_bole_47 ,