RetrogeneDB ID: retro_bole_17

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C3:47399636..47401208(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo3g129960
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo5g004190
• Aliases: None
• Description: None

Sequence

>retro_bole_17
ATGGCCACTGCTTCAGGTGCTTTTAAGTCTAGGGCAAATCACAGGAAGCAAATAGAATTAGAAGAAGCTCGTAAAGCTGG
GCTTGCTCCAGCAGAAGTAGATGAGGATGGAAAGGAAATCAATCCTCACATACCTCAGTACATGTCCTCTGCTCCATGGT
ATCTCAACTCTAAGAAACCGAGCTTGAAGCATCAAAGGAACTGGAAGAATGATCTCAATAGCAAAAGTACATGCTACGAC
AGAGGCGCAAAGATGTTTCAAGCTGAAAAATACAGGAAGAAAGCATGTCAAAACTGTGGTGCAATGTCTCATGATGTGAA
ATCATGTATGTATAGACCTCGTAAGGTCGGAGCCAAATTCACAAACATGTACATTGCACCGGATGAGAAGGTCGAGAGTC
TGAAACTCGACTATGCTGCCAAGAGGGACCGATGGAACGGTTATGATACTTCAGACTACCACCGTGTGGTAGAGCGCTAT
GAAGCAAGAGAGAATGCACGAAAGAAGTACCTAAAGGAGCAGAAGATTAAGAAACTAGAAGAGAATGATGGAGACGAAGA
TGAAGACGACGACGGCTTAAGAGTGGATGAAGCCAAGGTTGATGAGAGCAAGCAGATGGACTTTGCAAAGGTAGAAAAGC
GTGTTAGAACAAGTGGTGGTGGTAGCACAGGAACTGTAAGGAATCTACGTATCAGGGAAGACACTGCCAAGTATCTATTG
AACCTTGATGTCAACTCGGCTCACTACGACCCTAAAACAAGATCCATGCGTGAGGACCCGCTTCCAAATACAGATCCGAA
TGAGAAATTTTATTTGGGAGATAATCATTATAGAAACAGTGGGCAGGCTCTAGAGTTCAAACAGATGAACATCCACTCAT
GGGAAGCTTTTGACAAGGGACAAGACACGCATATGCAAGCGGCTCCATCCCAAGCTGAGTTGCTCTACAGGAACTTTAAG
GATGCTAAGGCCAAACTGATATCTCAAACAAAGGACTCACTTATGGAGAAGTATGGGAATGCTTCCACAGAGGATGACAT
CCCCATGGAGATTTTGCTTGGGCAAAGCGAAAGACAAGTAGAGTATGACCGTTCAGGGAGGATTATAAAGGGACAGGAGG
TGATACTTCCAAAGAGCAGATACGAAGAAGATGTTTATGCTAACAATCACACTAGTGTTTGGGGCTCATGGTGGAAAGAA
CAGCAGTGGGGATATAAATGTTGCAAGCAAACCATTCGCAATAGCTACTGTACAGGTTCTTCTGGAATTGACGCTGCAGA
GGCTTCCCTTGATCTGATGAACGCTAATATTGTTCGCACTGAATTGAGACCAAATACGGTTGAAGAGAAGAGAATGGCAA
CGTGGGGAACTGACATCCCTGGTGATTTGGAATTGAACAAGGATGTACTTTCTAATGCTCTTAAAAAGGAGGATGAGCTT
AAGAGAGAAGAAAAAGATGAGAGGAAACGAAAATACAATGTCAAATACAACAATGATGTGACTGTGGAAGAGATGGAAGC
TTATAGGATGAAGAGAGCTCACCACGAGGATCCAATGAAAGAGTTCCTCTGA

Alignment

ORF - retro_bole_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.4 %
• Parental protein coverage: 68.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEQQIKKLEEKNNNQEGDDAASDGDEEDDDLRVDEAKVDESRQMDFAKVEKRVRTTGGGSTGTVRNLRIR
          .E...KK...............D.DE.DD.LRVDEAKVDES.QMDFAKVEKRVRT.GGGSTGTVRNLRIR
Retrocopy RENARKKYLKEQKIKKLEENDGDEDEDDDGLRVDEAKVDESKQMDFAKVEKRVRTSGGGSTGTVRNLRIR

Parental  EDTAKYLLNLDINSAHYDPKTRSMREDPLPDADPNDKFYLGDNQYRNSGQALEFKQMNIHSWEAFDKGQD
          EDTAKYLLNLD.NSAHYDPKTRSMREDPLP..DPN.KFYLGDN.YRNSGQALEFKQMNIHSWEAFDKGQD
Retrocopy EDTAKYLLNLDVNSAHYDPKTRSMREDPLPNTDPNEKFYLGDNHYRNSGQALEFKQMNIHSWEAFDKGQD

Parental  MHMQAAPSQAELLYKNFKVAKDKLKTHTKDTIMEKYGNASTEDEIPMELLLGQSERQVEYDRAGRIIKGQ
          .HMQAAPSQAELLY.NFK.AK.KL...TKD..MEKYGNASTED.IPME.LLGQSERQVEYDR.GRIIKGQ
Retrocopy THMQAAPSQAELLYRNFKDAKAKLISQTKDSLMEKYGNASTEDDIPMEILLGQSERQVEYDRSGRIIKGQ

Parental  EVILPKSKYEEDVLANNHTTVWGSWWRDHQWGYRCCQQTIRNSYCTGSAGIEAAEASLDLMKANIARKEA
          EVILPKS.YEEDV.ANNHT.VWGSWW...QWGY.CC.QTIRNSYCTGS.GI.AAEASLDLM.ANI.R.E.
Retrocopy EVILPKSRYEEDVYANNHTSVWGSWWKEQQWGYKCCKQTIRNSYCTGSSGIDAAEASLDLMNANIVRTEL

Parental  CEDSPKKVEEKKMAAWGTDVPEDLELNEEALANALKKEDERKREEKDERKRKYNVKYTNDVTPEEMEAYR
          ....P..VEEK.MA.WGTD.P.DLELN...L.NALKKEDE.KREEKDERKRKYNVKY.NDVT.EEMEAYR
Retrocopy ---RPNTVEEKRMATWGTDIPGDLELNKDVLSNALKKEDELKREEKDERKRKYNVKYNNDVTVEEMEAYR

Parental  MKRVHHEDPMKDFM
          MKR.HHEDPMK.F.
Retrocopy MKRAHHEDPMKEFL

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_17 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	Bo5g004190	1 retrocopy	retro_bole_17 ,