RetrogeneDB ID: retro_bole_64

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C8:10187686..10188776(+)
• 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_64
AACAAATGGCAGGTGAAGATATTGAAGAAGGATCATACATGTGTTCCTACGGTACTCGTGAGATGCTCAAAGTTCCACAA
ATAACTCGCTTGTTTGTTGACAAGATCAGAGAAGAGCCAGAGTATTTCATGCCCATGAAGATTGAGGAGCTGGTTATGGA
GAAGTGGAAGCTCAGTGTTAGTAGGCCGCAATGCCAACATGCTAGGAACAAAGCGCTCAGATGGATTGAAAGAGAGTATG
ATGAGCAGTTTGGACGGTTGAGGGATTACTGCGCTGAGATAAGAAGCTCGAATGTTAATTCTTCTGTTGAGCTTGACTGC
CTGAGAAATGATGATGGGATCGAAGTTTTCAACAGATTTTATGTTTGTTTTGACATTCTGAGGAGAACCTGGAAAGAAAC
GTGCATGCCACTAATTGGAGTAGATGGTTGTTTCTTGAAGTCTAGGATGAAAGGACAGCTTCTAGTGGCTATGGGTCGTG
ATGCCGGTAACGCCATTTACCCTATCGCATGGGCTGTGGTACAAGTAGAAAACACCAACAATTGGTTGTGGTTTGTGAGA
AAGATCAAGGTTGATCTAGGACTTGATGTAGGAGAGGGTTATGTTATGGTTTCAGATCGTCAAAAGGGATTGATTGCAGC
TGTGAAGAGAGAATTGAGCATAGGATGTGTGTCAGACACATCTATGGCAACTTGAAGAAACACCATGGGAAGAAACCTGA
AATGAAGCTAAAGATTTGGAACCTTGCTTGGAGCTACAATGATGCTGATTACAAAGCAAATCTCAAAGACATTGAGCGGT
ATGATCAAGATGTTTATGACGACGTGATGAAGGCAAAGCCAGAGAAGTGGTGTAGGGCATTCTACAAGCTTGGACCTTTT
TGTGAAGACGTGGAGAATAACTCAACTGAATCTTTCAACAACTCCATATGTAAAACCCGAGACAAGCCCTTTGTACCTAT
GTTAGAGACAATAGCTCGCTTGGCAATGGTTCGTATAGCGAGAAGAGATGTCATCTGCAGCAGCCACGAAGGGATTTGCA
CACCGTATGTCATTGAGATGCTCGAGAGTTTGCATGAGAAAGGTTTAGAG

Alignment

ORF - retro_bole_64 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.23 %
• Parental protein coverage: 57.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NVWKVRVFVENHSCVPN-GECSMLKVPQIARLFVDKIREEPDYYMPMKIEQLVLEKWGITVSRAQCQAAR
          N.W.V......H.CVP..G...MLKVPQI.RLFVDKIREEP.Y.MPMKIE.LV.EKW...VSR.QCQ.AR
Retrocopy NKWQVKILKKDHTCVPT<GTREMLKVPQITRLFVDKIREEPEYFMPMKIEELVMEKWKLSVSRPQCQHAR

Parental  TKALKWIEFEYDHQFARLRDYAAEILESNKDSTVVIETLKNTYGKDEFNRFYICFDNIRRTWKETCRPLL
          .KAL.WIE.EYD.QF.RLRDY.AEI..SN..S.V....L.N..G...FNRFY.CFD..RRTWKETC.PL.
Retrocopy NKALRWIEREYDEQFGRLRDYCAEIRSSNVNSSVELDCLRNDDGIEVFNRFYVCFDILRRTWKETCMPLI

Parental  GVDGCFVKHKIKGQVLVALGRDADNAIYPVAWGVVQVENTDNWLWFVRMIREDLGLDDGDGFVIVSDRQ-
          GVDGCF.K...KGQ.LVA.GRDA.NAIYP.AW.VVQVENT.NWLWFVR.I..DLGLD.G.G.V.VSDRQ.
Retrocopy GVDGCFLKSRMKGQLLVAMGRDAGNAIYPIAWAVVQVENTNNWLWFVRKIKVDLGLDVGEGYVMVSDRQ<

Parental  KGLIAAVKEELPKVEHRKCVRHIYENLKKKHGSKSDMKSYLWSLAWSYNEAEYKERLDRILNYDVGVYDD
          KG......E.....EHR.CVRHIY.NLKK.HG.K..MK...W.LAWSYN.A.YK..L..I..YD..VYDD
Retrocopy KGIDCSCEE---RIEHRMCVRHIYGNLKKHHGKKPEMKLKIWNLAWSYNDADYKANLKDIERYDQDVYDD

Parental  VMKTNPKSWCRAYHRLGPYCEDVENNSTESFNNTIGKARELPFVPMFETIRRLAMARIAKRSAISHAHKG
          VMK..P..WCRA...LGP.CEDVENNSTESFNN.I.K.R..PFVPM.ETI.RLAM.RIA.R..I...H.G
Retrocopy VMKAKPEKWCRAFYKLGPFCEDVENNSTESFNNSICKTRDKPFVPMLETIARLAMVRIARRDVICSSHEG

Parental  ICTPYATEFLKVEKKKATE
          ICTPY..E.L.....K..E
Retrocopy ICTPYVIEMLESLHEKGLE

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_64 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 ,