RetrogeneDB ID: retro_bole_62

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C7:31843585..31845043(-)
• 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_62
GGTACTTGCGAGATGCTTAATGTTCCACAAATAGCTCGCTTGTTTGTTGACAAGATCAGAGAAGAACCAGAGTATTTCAT
GCCCATGAAGATTGAGCAGCTAGTAATGGAGAAATGGAAGATCAGTGTTAGTAAGCCGCAATGCCAACATGCTAGGAACA
AGGCCCTTAGATGGATTGAAAGAGAGTACGATGAGCAGTTTGGACGGCTGAGGGATTACTGCTCTGAGATAAGAAGCTCG
AATGTTAATTCTTCTGTTGAGCTTGATTGCCTGAAAAATGATGATGGGATAGACGTTTTCAACAGATTTTATGTCTGTTT
TGACATTCTGAGGAGAAACTGGAAAGAAACGTGTAGGCCACTAATTGGAGTAGATGGTTGTTTCTTGAAGTCTAGGATGA
AAGGGCAGCTGCTAATGGCTTTGGGTCGTGATGGCAATAACGCCATTTACTGTATCGCATGGGTTGTGGTACAAGTAGAG
AACAAAGTCAATTTGTTGTGGTTTGTGGAAAAGATCAAGGTTGATCTAGGACTAGACAAAGGAGATGGTTATGTTATGGT
TTTTGATAGTCAAAAGGGATTGATTGCAGTTGTGAAGAGAGAACTGCCGCGAATTGAGCGTAGAATGTGTGTTAGACACA
TCTACGGTAACTTAAAAAAGAACCATGGGAAGAAACCTGAAATGAAAAAACTGATTTGGAACCTTGCTTGGAGCTACAAT
GACGCTGATTACAAAGAAAATCTTTTAGAGATTGAGCGATATGATCAAGATGTTTATGACGACGTTTTGAAGACAAAGCC
AGAGAAGTGGTGTAGGGAATTCCACAAGCTTGGACCTTACTGTGAAGACGTCGAGAACAATTCCACTGAATCTTTCAACA
ACTCCAAAGCCCGAGACAAGCCCTTTGTGCCTATGTTGGAGACAATAGCTTGCTTGGCGATGGTTCGTATAGCGAAAAGG
GATGTTATTTGTACCAGCCACAAAGGGATTTGCACACCGTATGTCACTGAGATGCTCGAGACTTTGCATGAGAAAGCCTC
TTTATGCATGGTTAGACCATCTATCAACCAGACGTTTGGAGCTACTACTAATGGCTGTCAACATAGGGTGAGCTTGGAAA
ATAGAACTTGTAGTTGCAGGAGATGGGAGATTACAGGGATTCCTTGTGAACACGCCTATGGAGTTATGTTGTCGAAAGGT
TTAAAGGCTCAAGACTATGTTGTTCACTGGTTTCAGACAAGTACGTGGAAGCGTACATATGCTGTAGGGATTGTGCCATT
GCGTGGAGCAAATTTCTGGCCTGTAGGACTGGAACCATCTATAATTGAACCTGAGATCTCAGATCAACCAGGCTGTAAGA
AGGTGACTAAAGCGGATAAAAAGAGAAAGAGAGGAGTCAATGAATCACCATCGAAGAAAAAAGAGAAGTTCTTGAAGCGG
ATCATGCACTGTGGGATA

Alignment

ORF - retro_bole_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.52 %
• Parental protein coverage: 76.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GECSMLKVPQIARLFVDKIREEPDYYMPMKIEQLVLEKWGITVSRAQCQAARTKALKWIEFEYDHQFARL
          G.C.ML.VPQIARLFVDKIREEP.Y.MPMKIEQLV.EKW.I.VS..QCQ.AR.KAL.WIE.EYD.QF.RL
Retrocopy GTCEMLNVPQIARLFVDKIREEPEYFMPMKIEQLVMEKWKISVSKPQCQHARNKALRWIEREYDEQFGRL

Parental  RDYAAEILESNKDSTVVIETLKNTYGKDEFNRFYICFDNIRRTWKETCRPLLGVDGCFVKHKIKGQVLVA
          RDY..EI..SN..S.V....LKN..G.D.FNRFY.CFD..RR.WKETCRPL.GVDGCF.K...KGQ.L.A
Retrocopy RDYCSEIRSSNVNSSVELDCLKNDDGIDVFNRFYVCFDILRRNWKETCRPLIGVDGCFLKSRMKGQLLMA

Parental  LGRDADNAIYPVAWGVVQVENTDNWLWFVRMIREDLGLDDGDGFVIVSDRQKGLIAAVKEELPKVEHRKC
          LGRD..NAIY..AW.VVQVEN..N.LWFV..I..DLGLD.GDG.V.V.D.QKGLIA.VK.ELP..E.R.C
Retrocopy LGRDGNNAIYCIAWVVVQVENKVNLLWFVEKIKVDLGLDKGDGYVMVFDSQKGLIAVVKRELPRIERRMC

Parental  VRHIYENLKKKHGSKSDMKSYLWSLAWSYNEAEYKERLDRILNYDVGVYDDVMKTNPKSWCRAYHRLGPY
          VRHIY.NLKK.HG.K..MK...W.LAWSYN.A.YKE.L..I..YD..VYDDV.KT.P..WCR..H.LGPY
Retrocopy VRHIYGNLKKNHGKKPEMKKLIWNLAWSYNDADYKENLLEIERYDQDVYDDVLKTKPEKWCREFHKLGPY

Parental  CEDVENNSTESFNNTIGKARELPFVPMFETIRRLAMARIAKRSAISHAHKGICTPYATEFLKVEKKKATE
          CEDVENNSTESFNN...KAR..PFVPM.ETI..LAM.RIAKR..I...HKGICTPY.TE.L.....KA..
Retrocopy CEDVENNSTESFNNS--KARDKPFVPMLETIACLAMVRIAKRDVICTSHKGICTPYVTEMLETLHEKASL

Parental  CTITRSTNGMYEAKLGGCTHRVSSDRWTCTCMKFEICGIPCEHAYGVILHKKLKAEDFVCKWFRTSMWRR
          C....S.N....A...GC.HRVS....TC.C...EI.GIPCEHAYGV.L.K.LKA.D.V..WF.TS.W.R
Retrocopy CMVRPSINQTFGATTNGCQHRVSLENRTCSCRRWEITGIPCEHAYGVMLSKGLKAQDYVVHWFQTSTWKR

Parental  NYTDCLIPVRGARFWPQTSAPDVHIPPDPDQPGRKKLPKAEKKRKKPANESPTKKQPKHKKRIMHCEV
          .Y.....P.RGA.FWP....P....P...DQPG.KK..KA.KKRK...NESP.KK..K..KRIMHC..
Retrocopy TYAVGIVPLRGANFWPVGLEPSIIEPEISDQPGCKKVTKADKKRKRGVNESPSKKKEKFLKRIMHCGI

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_62 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 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,