RetrogeneDB ID: retro_bole_59

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C6:15858670..15859601(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo3g123420
• Aliases: None
• Description: None

Sequence

>retro_bole_59
ACCCCTTTTAGAGAAGAAGCTCTGGCGTCTTGTTCAATATCCAGATTCATTAGTGGCGAGAGTTCTTCGGGGAAAATATT
ACCTTCTCAGTTCGCCCTTGCGAATTGGCGCGGCGGATAACCCATCTTATGTTTGGAGAAGTATTATAGCGGCAAGGAAG
CTACTACTTTTGGGTATCAAAAGCAAAGTGCATTTAGGATATGAAATTAATGTGTGGCATGATCCGTGGATTTCCTCAAC
ACCAGCAAGGCCGGCTCGTCCCAGGGTCCCAGTAGTAAATCTGAAGATGATTGTAAGTAGCCTTATTAATTTTGAATCAA
AGGAGTGGGATGCTCGACTACTGGCACAATATGTAGACAAAGAGGACATATCGATGATTCAGAGTTTGGCCATAAGCCCT
ACTCATCGACGGGATACCTTTTGCTGGAGCTACACCATAAATGACCAATACACTGTCAAGTCTGGATACTGGGTTGCTAC
AAATATAATGACAGCTGACGAGGAAAAATAAGTCCTACAGCCCAGCATAACCGAACTTCAAGCCTATACTTGGAAAGTGA
ATGCACCACAAAAGATTCGCCATCTTCTATGGCAATTAATTTCAGGCCAGGTAGCGGTAACAATGAATCTAGTACGTCGC
AATATACAATGTGATAACTATTGTCCAAGATGTGGAGAGCCAGAATAAAATGTTACTCATGTGATCTTCGAATGCCCACC
GGCATTAAAAGCATGGGCATTATCATCAACGCCGTCAAGTTCTCAAACCTTCCCTATATCAAGTATGTATGCCAATATGG
ACTATCTGTTTTGGAGAAAGAATACTAAGCTAGAAGATGATAGAGACCCTTATCCCTGGATAATCTGGTATATTTGGAAG
GAAAGGAATGATAAGCTATTCAGAGGTATATATAGGGACCCATTGGAATTG

Alignment

ORF - retro_bole_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.4 %
• Parental protein coverage: 73.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TPFLAKSCQIGEVS-DSLVARVLREKYYRLSLPLRTGAVDTPLYVWTSIIAARKLLLLGIRSKVHSGYEI
          TPF..........S.DSLVARVLR.KYY.LS.PLR.GA.D.P.YVW.SIIAARKLLLLGI.SKVH.GYEI
Retrocopy TPFREEALASCSIS>DSLVARVLRGKYYLLSSPLRIGAADNPSYVWRSIIAARKLLLLGIKSKVHLGYEI

Parental  NVWEDPWIPSTPGRPARSQVPVVHPKMTVSSLIDFESKEWDARLLEQYVDQVDIPMIMSLAISPTHRRDT
          NVW.DPWI.STP.RPAR..VPVV..KM.VSSLI.FESKEWDARLL.QYVD..DI.MI.SLAISPTHRRDT
Retrocopy NVWHDPWISSTPARPARPRVPVVNLKMIVSSLINFESKEWDARLLAQYVDKEDISMIQSLAISPTHRRDT

Parental  FCLSYTKNGQYTVKYGYWVATNLMRTDEDLEVLQPSITKLQAFAWTVNASQNICHLIWQLISGQVAVTRN
          FC.SYT.N.QYTVK.GYWVATN.M..DE...VLQPSIT.LQA..W.VNA.Q.I.HL.WQLISGQVAVT.N
Retrocopy FCWSYTINDQYTVKSGYWVATNIMTADEEK*VLQPSITELQAYTWKVNAPQKIRHLLWQLISGQVAVTMN

Parental  QVYRNMRCDNYCPRCGEPEEIVTHVIFECPPALQAWTLSSTPSSPQSFHVPSVYSNMDYIFWRKNNIMKP
          .V.RN..CDNYCPRCGEPE..VTHVIFECPPAL.AW.LSSTPSS.Q.F...S.Y.NMDY.FWRKN...K.
Retrocopy LVRRNIQCDNYCPRCGEPE*NVTHVIFECPPALKAWALSSTPSSSQTFPISSMYANMDYLFWRKNT--KL

Parental  EDDRDPYPWIIWYIWKARNDKLFRGIDRDPLKL
          EDDRDPYPWIIWYIWK.RNDKLFRGI.RDPL.L
Retrocopy EDDRDPYPWIIWYIWKERNDKLFRGIYRDPLEL

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_59 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	Bo3g123420	1 retrocopy	retro_bole_59 ,