RetrogeneDB ID: retro_bole_34

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C5:39414780..39415464(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo5g127220
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo5g136540
• Aliases: None
• Description: None

Sequence

>retro_bole_34
ATGATGTTATCTTCTCTGGTTCCTCTGCAACTTCCATCTCGGATGCAAACTCATCTCTGGTATATGTTACCAAACGAAGT
GAAGAGCGAGTCTCTTCTAAAACACTACACTCAGCTTCTCTCACAACAGGAGAAAGATAGTATCTTTGGAATGCAAAGTG
ATGCGCTTAAGAAGAAGAATGCATTGCTTGCTCGCACCTTGGTTCGAACCACAGTGGCAAGATATCAGACAAACAACAAC
AACGACACTGTGGTGGATCCAAGATCGTTGAAGTTCAAGAAGAACCTGTACGGAAAGCCTGAAGTAGATGGGGAGGTTGA
TACTACTACTAATTATCCTAAACTGAAGTTCAACATCTCACACACGGATTCATTGATAGCCTGTGGAGTAACAGTAAACG
TTCCGGTTGGTATTGACGTTGAAGACAAGACAAGGAAGATGAGAAACGATGTGTTATCACTTGCAAAGAGATTTTACTCG
TCTGAAGAAGTTAAGTTTATGTCAAGTATAGCAGGTACTGAGGCTCAGCGTAAGGAGTTTATAAAGCTATGGACTCTCAA
AGAAGCTTATGTGAAAGCATTAGGGAAAGGCTTCTCTGCTTCACCTTTTAATACTTTCTCAATCATCCGGTCCGAGGCTG
CTAAAAACTACAGAATCCAACTTTTCACACTTTTGATCTTCTGA

Alignment

ORF - retro_bole_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSLIPLQLPSRRETHLWYVIPDEVKSTSLLKRYSQLLSPIEKDGVDQMRGDELKK-NALLARTLVRTTI
          L.SL.PLQLPSR..THLWY..P.EVKS.SLLK.Y.QLLS..EKD....M..D.LKK.NALLARTLVRTT.
Retrocopy LSSLVPLQLPSRMQTHLWYMLPNEVKSESLLKHYTQLLSQQEKDSIFGMQSDALKKKNALLARTLVRTTV

Parental  ARYQTNKE----VDPRSLMFKKNVYGKPEVDWQ---NCNNQPLHFNISHTDSLIACGVTVHVPVGIDVED
          ARYQTN......VDPRSL.FKKN.YGKPEVD.......N...L.FNISHTDSLIACGVTV.VPVGIDVED
Retrocopy ARYQTNNNNDTVVDPRSLKFKKNLYGKPEVDGEVDTTTNYPKLKFNISHTDSLIACGVTVNVPVGIDVED

Parental  KERKIKHDVLAFAKRFYSADEVNVLATILDPEVQRKEFIKLWTLKEAYVKALGKGFSAAPFNTFTI
          K.RK...DVL..AKRFYS..EV.....I...E.QRKEFIKLWTLKEAYVKALGKGFSA.PFNTF.I
Retrocopy KTRKMRNDVLSLAKRFYSSEEVKFMSSIAGTEAQRKEFIKLWTLKEAYVKALGKGFSASPFNTFSI

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_34 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	Bo5g136540	1 retrocopy	retro_bole_34 ,