RetrogeneDB ID: retro_bole_16

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C7:38185547..38186405(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo7g097940
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo3g061430
• Aliases: None
• Description: None

Sequence

>retro_bole_16
ATGAGAACACTAATCTCTCCATCTCTTCCTCCCCTCTTCTCTCTCCACCTCCCTAGACCTTCCCTCTTCTCTAGAGCTCT
TCGCGCCTCCCGCTACCCTCTCACAGCTTCCGCCTTCTCGCTCAACAGACTCCCCACTAATCCGCATCACTCGTCAGCTT
CACGCCGCGAATTACAGACGGAGGCGGCGTCTAAGCCCTCCTCTGCTCCTCCCGGGGAGATACACGTCGTCGTCGGTCCA
ATGTTCTCCGGGAAAACCACAACGCTTCTCCGCCGAATCCTCTCGGAGAGGGAGAGCGGGAAGAAGGTAGCCGTCATCAA
ATCGGATAAAGACGATAGGTACTGTGCCGAATCGATCGTTACTCACGACGGAGAGAAGTTCCCTTGCTGGGCTCTTCCCG
ATCTATCCTCTTTCAAGGAGAGATTCGGTTTCGATGCGTATAGGAATCAGTTAGACGTGATTGGGATCGACGAGGCTCAG
TTCTTCGGAGACCTCTACGAGTTTTGCCGCGAGGCGGCTGATAAGGAGGGTAAAACGGTAATTGTAGCGGGATTGGACGG
CGATTATCTGAGGAGGAGGTTCGGTTCGGTGCTGGATTTGGTTCCGATTGCGGATACGGTTACGAAGCTGGCGTCGAGGT
GTGAGGTTTGCGGGAAGAGAGCTTCGTTTACGCTGAGGAAGACGGAGGAGAGGGAGACAGAGTTGATCGGTGGAGCGGAG
GTGTATATGCCTGTGTGTCGGAGTCATTATGTTAGCGGTCAAGGCGTTTTGGAGACCGCTCGCGCCGTTTTGGATGCTTC
TTCCCAACGAAACGCGACGCGCGATTTAGAAGCAACGAGTCTCTCCCCTCCGTTTTAA

Alignment

ORF - retro_bole_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.34 %
• Parental protein coverage: 80.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAIHVITGPMFSGKSTSLLRRIKSEISLGRSVAMVKSSKDTRYAKDSVVTHDGIGFPCWAIPDLMSFPDM
          G.IHV..GPMFSGK.T.LLRRI.SE...G..VA..KS.KD.RY...S.VTHDG..FPCWA.PDL.SF...
Retrocopy GEIHVVVGPMFSGKTTTLLRRILSERESGKKVAVIKSDKDDRYCAESIVTHDGEKFPCWALPDLSSFKER

Parental  FGQDAY-DKLDVIGIDEAQFFGDVYEFCCKAADDNGKTVIVAGLDGDYLRRRFGALLDIVPIADSVTKLT
          FG.DAY...LDVIGIDEAQFFGD.YEFC..AAD..GKTVIVAGLDGDYLRRRFG..LD.VPIAD.VTKL.
Retrocopy FGFDAYRNQLDVIGIDEAQFFGDLYEFCREAADKEGKTVIVAGLDGDYLRRRFGSVLDLVPIADTVTKLA

Parental  ARCEVCGQKAFFTLRKTCDTKTELIGGADVYMPVCRKHYVNNQIVIKASKKVLDSDKER
          .RCEVCG..A.FTLRKT....TELIGGA.VYMPVCR.HYV..Q.V......VLD....R
Retrocopy SRCEVCGKRASFTLRKTEERETELIGGAEVYMPVCRSHYVSGQGVLETARAVLDASSQR

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_16 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G07800	1 retrocopy	retro_atha_9,
Brassica oleracea	Bo3g061430	1 retrocopy	retro_bole_16 ,
Brassica rapa	Bra001266	1 retrocopy	retro_brap_33,
Arabidopsis lyrata	fgenesh2_kg.3__818__AT3G07800.1	1 retrocopy	retro_alyr_19,