RetrogeneDB ID: retro_bole_50

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C4:37929857..37930840(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo2g149410
• Aliases: None
• Description: None

Sequence

>retro_bole_50
AAAAGACCACATCTATATTGGTTTCCTTGTGCATCACACTGCACTGATCTCATGTTGGAGAATATAGGAAAGATTCCTTT
AGTTAAGGCTGCAATAACAAGTTGCATCTTTTTGAATGGCTACATTTGTGGTCTACTTCTGTCGAGAATATGATGAGAAG
GTTCACAAACCAAAAATATTTGCATAGACCACCAGTTACTCGGTTTTTTACGTCATTCATCACACTTGGCCAATACTACC
ACCACAAGGATAACTTGAGAAAGTTTATAACTTCTCAAGATTGGATTGATTCAAAGTGGTCAAAAGAATTATGAGCAAAG
AAGGGGAAACAAATCAGTATGCAAGACAACTTCTGGAAAAAAGTTGTTTATGCAATCAAGTTGACTGGGCCATTAGTTAA
AGTTCTTCGATTGGTAGATGGGGATAAAAATCAGCGATAGGGTACATTTATTAAGTAATTGACAACGCTAAGGACACCAT
TACCAAATCCTTCCTCCATGAAGGAGATAAGTACAAGTGTATTTCTAAAATAATTGATGAAAGGTGGAACTGCCAATTCC
ATCAGCCTTTTACATGCTGCTGGCCACTTTTTGAATCTTGAATTTCAGTACAAAGGGCCTGGAGTGTATTGTGGAGAGCT
CATGACATGTTTACACAACACCTTTGAAAGATTGGTTCCTCAAGTTACAACATAAGATCAGATACTTAAAGAGCTAGATC
ATTTTAAGAATGCTTCTAGACTCTTTAGTAATACCATGAAGATAAGACAAAGGGCAACAAGGGGACCAAATGAGTGGTAG
CGGTCTTATGGAGCTTATACTCCAACACTTAGAGTTTTTGCTGTAAAAGTTCTTAGTCTCACGTGTAGCGCAACATGTTG
GGAGAGATATTGTAGTGTGTTTCAGCATCTCCATACCAAGAAAAGGAATCGATTGACTCAAGTCCAGTTGAATAACATGA
TTTTTGCTAAGTAAAATTGTGCT

Alignment

ORF - retro_bole_50 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.52 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRPHLYWTPCAAHCIDLMLEDIGEIPALKSAMKKCMFMNGYIYS-HVPLVNMMRKFTKQRNLHRPAITRF
          KRPHLYW.PCA.HC.DLMLE.IG.IP..K.A...C.F.NGYI........NMMR.FT.Q..LHRP..TRF
Retrocopy KRPHLYWFPCASHCTDLMLENIGKIPLVKAAITSCIFLNGYICG<STSVENMMRRFTNQKYLHRPPVTRF

Parental  ATSCITMTQFLKQQKPLRDMVNSAEWSESKWPKEAGARKVRQYLMQASFWKNIRRALKIMTPLVKVLRMV
          .TS.IT..Q.......LR....S..W..SKW.KE..A.K..Q..MQ..FWK....A.K...PLVKVLR.V
Retrocopy FTSFITLGQYYHHKDNLRKFITSQDWIDSKWSKEL*AKKGKQISMQDNFWKKVVYAIKLTGPLVKVLRLV

Parental  DGEK-KPAMGYIYAAMDRAKETIERDFKWNKEKYEEAFEIIDKRWQCQLHHP-LHAAGYFLNPSIHYKYP
          DG.K.K.A.GYIY...D.AK.TI...F.....KY.....IID.RW.CQ.H.P.LHAAG.FLN....YK.P
Retrocopy DGDK<KSAIGYIY*VIDNAKDTITKSFLHEGDKYKCISKIIDERWNCQFHQP>LHAAGHFLNLEFQYKGP

Parental  DDVRCAEVEGGLYNCIARLVPNTETQDKIMTELDSFKDASGIFGHDMAIRQRDIKAPAEWWFCYGSSAPN
          ..V.C.E....L.N...RLVP...T.D.I..ELD.FK.AS..F...M.IRQR....P.EW...YG...P.
Retrocopy G-VYCGELMTCLHNTFERLVPQVTT*DQILKELDHFKNASRLFSNTMKIRQRATRGPNEW*RSYGAYTPT

Parental  LRSFAVKILSLTCSATGCERNWSVFQLLHTKKRNRLAQHRLNNMVFVKYNRA
          LR.FAVK.LSLTCSAT..ER..SVFQ.LHTKKRNRL.Q..LNNM.F.K.N.A
Retrocopy LRVFAVKVLSLTCSATCWERYCSVFQHLHTKKRNRLTQVQLNNMIFAK*NCA

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_50 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	Bo2g149410	1 retrocopy	retro_bole_50 ,