RetrogeneDB ID: retro_bole_63

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C8:8290006..8291435(+)
• 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_63
AAGCTGTTTGTTGACAAGATCAGAGAAGAGCCAGAGTATTTCATGCCCATGAAGATTGAGGAGCTGGTTATGGAGAAGTG
GAAGCTCAGTGTTAGTAGGCCGCAATGCCAACATGCTAGGAACAAAGCGCTCAGATGGATTGAAAGAGAGTATGATGAGC
AGTTTGGACGGTTGAGGGACTACTGCGCTGAGATAAGAAGCTCGAATGTTAATTCTTCTGTTGAGCTTGACTGCCTGAGA
AATGATGATGGGATCGAAGTTTTCAACAGATTTTATGTCTGTTTTGACATTCTGAGGAGAACCTGGAAAGAAACGTTCAG
GCCACTAATTGGAGTAGATGATTGTTTCTTGAAGTCTAGGATGAAAGGAAAGCTTCTCGTGGCTTTGGGTCGTGATGCCG
ATAACGCCATTTACCCTATCGCATGGGCTGTGGTACAAGTAGAAAACAACAACAATTGGTTGTGGTTTGTGAGAAAGATC
AAGGTTGATCTAGGACTAGATGAAGGAGAGGGTTATGTTATGGTTTCAGATCGTCAAAAGGGATTGATTGCAGCTGTGAA
GAGAGCACTATCGCGAATTGAGCATAGGATGTGTGTCAGACACATCTATGGCAACTTGAAGAAACTCCATGGGAAGAAAC
CTGAAATGAAGCTAAAGCTTTGGAACCTTGCTTGGAGCTACAATGATGCTGATTACAAAGCAAATCTCAAATACTTTGAG
AGGTATGATCAAGATGTTTATGACTACGTGATGAAGGCAAAGCCAGGGAAGTGGTGTAGGGAATTCTACAAGCTTGGAAC
TTTTTGTGAAGACGTGGAGAATAGCTCAACTGAATCTTTCAACAACTCCATAGGTAAAGCCCGAGACAAGCCTTTTGTAC
CTATGTTTGAGACAATAGCTCGCTTGGCGATGGTTCGTATAGCGAGAAGAGATGTCATCTGCAGCAGCCACGAAGGGATT
TGCACACCGTATGTCATTGAGATGCTCGAGAGTTTGCATGAGAAAGCCTCGAAATGCATGGTTCAACCTTCCACCAACCA
GACATATGAATCTACTAGTAATGACTGTGTGCATAGGGTGAGCTTGGAAAATAAAACATGTAGCTGCAGAAGATGGGAGA
TTACAGGGATCCCTTGTGAGCACGCCTATGGAGTTATGCTGAAGAAAGGTTTAGAGGCTCAAGACTTTGTGGTTCACTGG
TTTAGGATAGCTACGTGGAGGCGTACGTATGCTGAAGGGATTGTACCTTTGCGTGGAGCAAAGTTCTAGCCCGTAGGACC
GGAACCATCTATAATTGAACCTGAGATCCCAGATCAACCAGACCATAAGAAGGAGACTAAAGCAGATAAAAAGAGAGAGA
AAGGAGTCAATGAATCACCATCGAAGAAAAAAAGAGAAGTTCTTGAAGGGGATAATGCACTGTGGGATA

Alignment

ORF - retro_bole_63 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.05 %
• Parental protein coverage: 74.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLFVDKIREEPDYYMPMKIEQLVLEKWGITVSRAQCQAARTKALKWIEFEYDHQFARLRDYAAEILESNK
          .LFVDKIREEP.Y.MPMKIE.LV.EKW...VSR.QCQ.AR.KAL.WIE.EYD.QF.RLRDY.AEI..SN.
Retrocopy KLFVDKIREEPEYFMPMKIEELVMEKWKLSVSRPQCQHARNKALRWIEREYDEQFGRLRDYCAEIRSSNV

Parental  DSTVVIETLKNTYGKDEFNRFYICFDNIRRTWKETCRPLLGVDGCFVKHKIKGQVLVALGRDADNAIYPV
          .S.V....L.N..G...FNRFY.CFD..RRTWKET.RPL.GVD.CF.K...KG..LVALGRDADNAIYP.
Retrocopy NSSVELDCLRNDDGIEVFNRFYVCFDILRRTWKETFRPLIGVDDCFLKSRMKGKLLVALGRDADNAIYPI

Parental  AWGVVQVENTDNWLWFVRMIREDLGLDDGDGFVIVSDRQKGLIAAVKEELPKVEHRKCVRHIYENLKKKH
          AW.VVQVEN..NWLWFVR.I..DLGLD.G.G.V.VSDRQKGLIAAVK..L...EHR.CVRHIY.NLKK.H
Retrocopy AWAVVQVENNNNWLWFVRKIKVDLGLDEGEGYVMVSDRQKGLIAAVKRALSRIEHRMCVRHIYGNLKKLH

Parental  GSKSDMKSYLWSLAWSYNEAEYKERLDRILNYDVGVYDDVMKTNPKSWCRAYHRLGPYCEDVENNSTESF
          G.K..MK..LW.LAWSYN.A.YK..L.....YD..VYD.VMK..P..WCR....LG..CEDVEN.STESF
Retrocopy GKKPEMKLKLWNLAWSYNDADYKANLKYFERYDQDVYDYVMKAKPGKWCREFYKLGTFCEDVENSSTESF

Parental  NNTIGKARELPFVPMFETIRRLAMARIAKRSAISHAHKGICTPYATEFLKVEKKKATECTITRSTNGMYE
          NN.IGKAR..PFVPMFETI.RLAM.RIA.R..I...H.GICTPY..E.L.....KA..C....STN..YE
Retrocopy NNSIGKARDKPFVPMFETIARLAMVRIARRDVICSSHEGICTPYVIEMLESLHEKASKCMVQPSTNQTYE

Parental  AKLGGCTHRVSSDRWTCTCMKFEICGIPCEHAYGVILHKKLKAEDFVCKWFRTSMWRRNYTDCLIPVRGA
          .....C.HRVS....TC.C...EI.GIPCEHAYGV.L.K.L.A.DFV..WFR...WRR.Y.....P.RGA
Retrocopy STSNDCVHRVSLENKTCSCRRWEITGIPCEHAYGVMLKKGLEAQDFVVHWFRIATWRRTYAEGIVPLRGA

Parental  RFWPQTSAPDVHIPPDPDQPGRKKLPKAEKKRKKPANESPTK-KQPKHKKRIMHCEV
          .F.P....P....P..PDQP..KK..KA.KKR.K..NESP.K....K..K.IMHC..
Retrocopy KF*PVGPEPSIIEPEIPDQPDHKKETKADKKREKGVNESPSK>XXEKFLKGIMHCGI

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_63 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,