RetrogeneDB ID: retro_bole_21

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C5:6762922..6763801(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo5g019920
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo3g046940
• Aliases: None
• Description: None

Sequence

>retro_bole_21
ATGGATCTTCCGCGAGACGTCGACGACTACATCAAGGACACGATCGACCACTCTCTGGGGATCCCGATCTCCATAGACGC
TCTCCAGAACAAACTCTCCGCGGCTCAAGAGTCTCAGCGTCGTCTTCGCGAACAGTACATGTCTCTAGTCTCCAGGTTGA
AAGAGAAAGAACAAATGATCGAACTCGCGAGATCGGAAGCGAGCATCAACGCTCAGGCCGTTAAGAAATTCGTCGAGGAG
AATCGGGAACTGAGCGGCGAGTGCGAGGATTTGGTGAAGCAGTGTAAGAAATGGGAAAGAGAGTGCTTTCTTTACCATCA
AGACCGTGAGGCGTTGATGGATTTCGGTAACGAGTCCGACGAGAGGGCGAGAGAAAGTGAATCTAGGGTTCGGGAATTAG
AGGAACAAGTGAGAACGATGTCTGATGTAATGAAGAAGCGTAAAGTGGAATCCGACAAGAAGTTAACGTCGTTAGAAGAA
GAGGAACGTTTGGTTGATTCAGTGTTGTCATCGTTTGTTAGCGAAGACGAGATTAAGTTTGGGCGCGTGTTCTTGGAGGC
GAACATTAAAGACCGGTCTTTGTTGAGCAGATGGGAGGAGTTGAAGCCGTCGACGCGAAAGGCTGTGTCTTTGGTTGCGA
TGGTGAAGAGGATTGAAAAGGAGAAAGAGTGCCTCATCTTGAATCTCGCTAAAGCCGAACAGGAAGTTGAGATTGTGTGC
GAGCAAAACAGAGAGCTAGATGAAAAGAACCGCAAGCTGTTGAAGCAATTTAGTAGTAGTAGCTATCTACAGTGTTCTGC
AGAGAGAAGCAAGTCCAAGAAGAGAAAGAGTCCTAAGATGATGAGCAGCAGCAGCCCAGGATCTATCAACGATATTTAA

Alignment

ORF - retro_bole_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.41 %
• Parental protein coverage: 85.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLSPEVDDYIKDTIDHSLGLPISIESLQTKLLAAEEAQRRLRDQYLALLSRSKEKDQVLERVRSEASMN
          M.L...VDDYIKDTIDHSLG.PISI..LQ.KL.AA.E.QRRLR.QY..L.SR.KEK.Q..E..RSEAS.N
Retrocopy MDLPRDVDDYIKDTIDHSLGIPISIDALQNKLSAAQESQRRLREQYMSLVSRLKEKEQMIELARSEASIN

Parental  AQALKKFVEENQKLAEECGNLLRQCKKWERECLLYHQDRDALMEFGNESDERARDAEARVRELEEEVARM
          AQA.KKFVEEN..L..EC..L..QCKKWEREC.LYHQDR.ALM.FGNESDERAR..E.RVRELEE.V..M
Retrocopy AQAVKKFVEENRELSGECEDLVKQCKKWERECFLYHQDREALMDFGNESDERARESESRVRELEEQVRTM

Parental  SEELQLCKQRQIGIEQVDNNCSPQEEDLLDSVLGSLISKDENTIGRLFLEANVQDQSCQALLSKWDRLKP
          S......K.R..............E..L.DSVL.S..S.DE...GR.FLEAN..D.S...LLS.W..LKP
Retrocopy SD---VMKKRKVESDKKLTSLEEEER-LVDSVLSSFVSEDEIKFGRVFLEANIKDRS---LLSRWEELKP

Parental  STQKVLSLVSVAKKFEKERECIIQNLAKAEQEAELVSIQNRKLDKENRKLLRQQLSPLGSSETSHKSASA
          ST.K..SLV...K..EKE.EC.I.NLAKAEQE.E.V..QNR.LD..NRKLL.Q..S...SS.........
Retrocopy STRKAVSLVAMVKRIEKEKECLILNLAKAEQEVEIVCEQNRELDEKNRKLLKQFSS---SSYLQCSAERS

Parental  KSNKRKCPKMMSS
          KS.KRK.PKMMSS
Retrocopy KSKKRKSPKMMSS

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_21 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	Bo3g046940	1 retrocopy	retro_bole_21 ,