RetrogeneDB ID: retro_bole_55

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C5:20835319..20837190(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo7g080770
• Aliases: None
• Description: None

Sequence

>retro_bole_55
GAAGATCGAAGAGAGCGTAACGACTACAACATTGAGAAAGAAGCCATGGACTTTGTTGATGAACATCCAGTGAAGCATAA
CTTGTATCCAGACATTGAAGATAATGAAGATGAAGAGGGAAAAGAAATTCAAAGGACTATCTACAGGCGCAATAATATTA
GGAGAGGCAACGGGGAGTTGTATGTTAGGCAAGTGTTCATCAGTGGATTTGCGTTTAAGGAAACAGTGCTCGACTATGCT
CTGAAAACAGGTCTGAACATCAAACAGAATCGATATGACAAGACAAAGATTGCATTTGTATGTGTAGGCAAAGGTTGCTC
TTGGCGCATTTTCTGCTCTTCCTCAGAAAAGTCTCCCAACAAGTGGCAGGTGAAGATATTGAAAAAGGATCATACCTGTG
TTCCTACGGGTACTTGCGAGATGCTTAAAGTTCCACAATTAGCTCGCTTGTTTGTTGACAAGATCAGAGAAGAACCAGAG
TATTTCATGCCCATGAAGATTGAGCAGCTAGTCATGGAGAAATGGAAGATCAGTGTTAGTAGGCCGCAATGCCAACATGC
TAGGAACAAGGCCCTTAGATGGATTGAAAGAGAGTATGATGAGCAGTTTGGATGGCTGAGGGATTACTGCTCTGAGATAA
GAAGCTCCAATGCTAATTCTTCTGTTGAGCTTGATTGCCTAAAAAATGATGATGGGATACACGTTTTCAACAGATTTTAT
GTCTGTTTTGACGTTCTGAGGAGAAACTGGAAGGAAACGTGCAGGCCACTAATTGGAGTAGATGGTTGTTTCTTGAAGTC
TAGGATGAAAGGGCAGCTTCTAGTGGCTTTGGGTCGTGATGGGGATAAGGCCATTTACCTTATCGCATGGACTGTGGTAC
AAGTAGAGAACAAAGTCAATTGGTTGTGGTTTGTGGAAAAGATCAAGGTTGATCTAGGACTAGACGAAGGAGATGGTTAT
GTTATGGTTTCAGATCGTCAAAAGGGATTGATTGCAGCTGTGAAGAGGGCACTACCGTGAATTGAGCATAGAATGTGTGT
TAGACACATCTACGGGAACTTGAAAAAGAACCATGGGAAGAAACCTGAAATGAAAAACTGATTTGGAACCTTGGTTGGAG
CTACAATGACGCTGATTACAAAGCAAATCTCTTAGAGATTGAGCGGTATGATCAAAATGTTTATGATGACGTTATGAAAA
CAAAGCCAGAGAAGTGGTGTAGAGCATTCCACAAGCTTGGACCTAACTGTGAAGATGTCGAGAACAACTCCACTGAATCT
TTCAACAACTCCATAGGTAAAACCCGAGACAAGCCCTTTGTGCCTATGTTGGAGACAATAGCTCGCTTGGCGATGGTTCG
TATAGCGAAAAGGGATGTTATTTGCACCAGCCACGAAGGGATTTGCACACCGTATGTCACTGAGATGCTCGAGACTTTGC
ATGAGAAAGCCTCTTTATGCACGGTTATACCGTCTACCAACCAGACATTTGGAGCTACTACTAATGGCTGTCAACATAGG
GTGAGCTTGGAAAATAGAACTTGTAGTTGCAGGAGATGGGAGATTACAGGGATTCCTTGTGAACACGCCTATGGAGTTAT
GTTGTCGAAAGGTTTAGAGGCTCAAGACTATGTTGTTCACTGGTTTCGGACAAGTACATGGAGGCGTACATATGCTGAAA
GGATTGTGCCATTGCGTGGAGCAAAGTTCTGGCCTGTAGGACCGGAACCATCTATAATTGAACCTGAGATCCCAGATCAA
CCAGGCCGTAAGAATGTGACTAAAACGGATAAAAAGAGAAAGAGAGGAGTCAATGAATCACCATCGAAGAAAAAAGAGAA
GTTCTTGAAGCGGATTATGCACTGTGGGGTA

Alignment

ORF - retro_bole_55 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.62 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEAEERDECEIEHLLNEFVDEPSIRHDQIPE---SDDEEEKGCKKKPPEVTHIKRGDGSLYKKHTFVNGV
          E...ER....IE.....FVDE....H...P......DEE.K...........I.RG.G.LY....F..G.
Retrocopy EDRRERNDYNIEKEAMDFVDEHPVKHNLYPDIEDNEDEEGKEIQRTIYRRNNIRRGNGELYVRQVFISGF

Parental  GFKDCVLNYALKTGHNIQQYMYDKDKIGFKCVGSNEGGSCEWKIYASVLS-SDNVWKVRVFVENHSCVPN
          .FK..VL.YALKTG.NI.Q..YDK.KI.F.CV....G..C.W.I..S....S.N.W.V......H.CVP.
Retrocopy AFKETVLDYALKTGLNIKQNRYDKTKIAFVCV----GKGCSWRIFCSSSEKSPNKWQVKILKKDHTCVPT

Parental  GECSMLKVPQIARLFVDKIREEPDYYMPMKIEQLVLEKWGITVSRAQCQAARTKALKWIEFEYDHQFARL
          G.C.MLKVPQ.ARLFVDKIREEP.Y.MPMKIEQLV.EKW.I.VSR.QCQ.AR.KAL.WIE.EYD.QF..L
Retrocopy GTCEMLKVPQLARLFVDKIREEPEYFMPMKIEQLVMEKWKISVSRPQCQHARNKALRWIEREYDEQFGWL

Parental  RDYAAEILESNKDSTVVIETLKNTYGKDEFNRFYICFDNIRRTWKETCRPLLGVDGCFVKHKIKGQVLVA
          RDY..EI..SN..S.V....LKN..G...FNRFY.CFD..RR.WKETCRPL.GVDGCF.K...KGQ.LVA
Retrocopy RDYCSEIRSSNANSSVELDCLKNDDGIHVFNRFYVCFDVLRRNWKETCRPLIGVDGCFLKSRMKGQLLVA

Parental  LGRDADNAIYPVAWGVVQVENTDNWLWFVRMIREDLGLDDGDGFVIVSDRQKGLIAAVKEELPKVEHRKC
          LGRD.D.AIY..AW.VVQVEN..NWLWFV..I..DLGLD.GDG.V.VSDRQKGLIAAVK..LP..EHR.C
Retrocopy LGRDGDKAIYLIAWTVVQVENKVNWLWFVEKIKVDLGLDEGDGYVMVSDRQKGLIAAVKRALP*IEHRMC

Parental  VRHIYENLKKKHGSKSDMKS-YLWSLAWSYNEAEYKERLDRILNYDVGVYDDVMKTNPKSWCRAYHRLGP
          VRHIY.NLKK.HG.K..MK....W.L.WSYN.A.YK..L..I..YD..VYDDVMKT.P..WCRA.H.LGP
Retrocopy VRHIYGNLKKNHGKKPEMKN<LIWNLGWSYNDADYKANLLEIERYDQNVYDDVMKTKPEKWCRAFHKLGP

Parental  YCEDVENNSTESFNNTIGKARELPFVPMFETIRRLAMARIAKRSAISHAHKGICTPYATEFLKVEKKKAT
          .CEDVENNSTESFNN.IGK.R..PFVPM.ETI.RLAM.RIAKR..I...H.GICTPY.TE.L.....KA.
Retrocopy NCEDVENNSTESFNNSIGKTRDKPFVPMLETIARLAMVRIAKRDVICTSHEGICTPYVTEMLETLHEKAS

Parental  ECTITRSTNGMYEAKLGGCTHRVSSDRWTCTCMKFEICGIPCEHAYGVILHKKLKAEDFVCKWFRTSMWR
          .CT...STN....A...GC.HRVS....TC.C...EI.GIPCEHAYGV.L.K.L.A.D.V..WFRTS.WR
Retrocopy LCTVIPSTNQTFGATTNGCQHRVSLENRTCSCRRWEITGIPCEHAYGVMLSKGLEAQDYVVHWFRTSTWR

Parental  RNYTDCLIPVRGARFWPQTSAPDVHIPPDPDQPGRKKLPKAEKKRKKPANESPTKKQPKHKKRIMHCEV
          R.Y.....P.RGA.FWP....P....P..PDQPGRK...K..KKRK...NESP.KK..K..KRIMHC.V
Retrocopy RTYAERIVPLRGAKFWPVGPEPSIIEPEIPDQPGRKNVTKTDKKRKRGVNESPSKKKEKFLKRIMHCGV

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_55 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo7g080770	4 retrocopies	retro_bole_55 , retro_bole_62, retro_bole_63, retro_bole_64,