RetrogeneDB ID: retro_bole_46

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C2:32939581..32940909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo1g118890
• Aliases: None
• Description: None

Sequence

>retro_bole_46
TATCTCTCGTCTATCGCCAGCGGAGACTTCAAAGTCGAGCCTCTAAAAGCCAAGCCCAAAAATGGCAAAAGTTGGAGCAA
AAATAAGGAAAGAAGAGCCCAGCGCAAGGCAACCAGGCAAAGGCCGACAAAACGAAAAACGACCATAGGACGAGGACAAG
GCTCTAAAGGATGATGGTAACGACTACTCTTCCGCTGACGAAGAACAGCCGACGAACCGCATGCGCATAGAGGTTATACT
CTCTCAACAAGCTCTATCATCCGACGAAGAAAATGATGACGCACCTTCATCCGGAGATTTGAGGGATGTACTCAAGCGAA
AGCTCGAGCCTGAATATAATAACGATCCAATAGATAATGATCTTTGGCTGACGTTTAACGCACGAAAGTCCAGACGTGTC
CTGACCAGCAATCCCGTCCCCGGACCGCATCCGAAACATTCGGGCAGCGATCTTCGATACAAGCTCAATGACAACATATG
CGATCTACGCGTCCTCCTCAACTGCTCGAAGCCGACAGACCTCTGGAGGCAGTTAGAACGAACTAAGACACCAGGCAGTT
CTACGCTGTCGCAAAACGACGACAACGCATCCGCTGACCTGCGCGCCTTTTTAAACTCCAAGAGGGCACACTCGAGGCCA
AAACTAAACGTCATCATGGGCGGCTACCCTCCTAGCGGTAATTCTGTTAGCTCTGTCAAGGATTACCTCCGGCAAGCCGC
GACATCGCAGAGGTGGCCGACTAAGTCACCCAATCACCCTCCGATAACCTTCTCGCCTAACGACACCGCTGGAATTCGTA
TCCCCCATAACGACCCCTTTCTTGTCGTCCTAGGGATTGGGGAGTACGGCGTCACAAAAGTACCCATCGAGACGGGAAGC
TCCGTCGACCTCATTTTCTGAGGAGCATTCCAAAAGATGGGCATCGATCTCAACGATATCAAGGCATCATCCAGAACATT
AACCGGATTCAATGGCTCCTCCTAAACAATACTAGGAACGATCCGTCTCTCATTACGTGCCTGCGGAGTTACTCGAACGG
TTAAGTTCGCTGTCGTCAGCACGAAGGTGCCTTATCATGCGATTCTTAGGACCCCATGGATTCACTCGATGCAGGCGGTC
CCATCCACCTATCACCAGTGCATCAAGTTCCCGGGAACGGATGGCGCAACTAAAACATTACGAGGAGATCAGCAGGCCAC
GCGAGACCTACTGATCGCCACCGTAATGCTCCAACGTTCTTCGCTACCCGTCAACTCTGTCTCTCCCCCGATCGCCAAAG
TCTGTCCTCAGAAGGAAGAAGTTCTCGAGTTACCCATCGATGCCACCG

Alignment

ORF - retro_bole_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.62 %
• Parental protein coverage: 52.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YMYVVNENNVPISTLVVRGEGWNKWSKNKERRAQRKAT-GKGRHSETQQRDDEEDAPKSNGKGESSADEE
          Y.............L.........WSKNKERRAQRKAT.GKGR..E.....DE..A.K..G...SSADEE
Retrocopy YLSSIASGDFKVEPLKAKPKNGKSWSKNKERRAQRKAT>GKGRQNE-KRP*DEDKALKDDGNDYSSADEE

Parental  QPANRRRIEVILSQQTLSSDDENDDTPVLEDLRDVLKRKFESENSNNSTHNDLRTMLNARKSRRISPGDP
          QP.NR.RIEVILSQQ.LSSD.ENDD.P...DLRDVLKRK.E.E..N....NDL....NARKSRR.....P
Retrocopy QPTNRMRIEVILSQQALSSDEENDDAPSSGDLRDVLKRKLEPEYNNDPIDNDLWLTFNARKSRRVLTSNP

Parental  DP---KERSNGDLRDKLNAGACDLRIRLNRSKPTDLRRRLEQTKTSNNDIPSSKNDSSVPTDLRAFLDSK
          .P......S..DLR.KLN...CDLR..LN.SKPTDL.R.LE.TKT.......S.ND.....DLRAFL.SK
Retrocopy VPGPHPKHSGSDLRYKLNDNICDLRVLLNCSKPTDLWRQLERTKTPGSST-LSQNDDNASADLRAFLNSK

Parental  QVKTRQQLNVIMGGSPPCGNSVCSIKDYRRQVATSQRWPTRPPNHPPITFSPDDAEGVHLPHNDPLLVVL
          ....R..LNVIMGG.PP.GNSV.S.KDY.RQ.ATSQRWPT..PNHPPITFSP.D..G...PHNDP.LVVL
Retrocopy RAHSRPKLNVIMGGYPPSGNSVSSVKDYLRQAATSQRWPTKSPNHPPITFSPNDTAGIRIPHNDPFLVVL

Parental  AIGEYDATKVLIDTGSSVNLIFRGTLQKMGVDLNDIKPSSRTLTGFNESSKTTLGTIRLPVRACGVTQTV
          .IGEY..TKV.I.TGSSV.LIF.G..QKMG.DLNDIK.SSRTLTGFN.SS.T.LGTIRL..RACGVT.TV
Retrocopy GIGEYGVTKVPIETGSSVDLIF*GAFQKMGIDLNDIKASSRTLTGFNGSS*TILGTIRLSLRACGVTRTV

Parental  KFAVVSTKAPHHAILGTPWIHSMQVIPSTYHRCVKFPGTDGKIKTLRGDQKAVRELLVATVKLQRTSLSV
          KFAVVSTK.P.HAIL.TPWIHSMQ..PSTYH.C.KFPGTDG..KTLRGDQ.A.R.LL.ATV.LQR.SL.V
Retrocopy KFAVVSTKVPYHAILRTPWIHSMQAVPSTYHQCIKFPGTDGATKTLRGDQQATRDLLIATVMLQRSSLPV

Parental  NFVSPPTYKAC-SQEGESS-PELRNMPP
          N.VSPP..K.C.S.EG.SS......MPP
Retrocopy NSVSPPIAKVC<SSEGRSS<SSYPSMPP

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_46 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	Bo1g118890	1 retrocopy	retro_bole_46 ,