RetrogeneDB ID: retro_bole_6

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C5:7174404..7175943(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo5g020710
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo1g091740
• Aliases: None
• Description: None

Sequence

>retro_bole_6
ATGGCAGAACTTGAAGATTCTTTCCTCGCAGAGATTGACGAGTTATCCGACTATGAAGAAGCAGGATTCGAAGAGAACGC
TGGAAGCTATGGAGGAGATATCGCCATGGACATGTCAGACTTGGAAACCCTAAAGTCTGACGATGATCTCGACAGCGTCT
CTAAGCTACAGAAAACTCAAAGATACGCTGATATAATGAACAAGGTGGAAGACGCTCTCGGCAAGGATTCGTATGGAGCT
TTGTCAGAAGACGATCCTCTATACAAACTAATCGTGGACTGCAACAAGCTCTCAGTCGATATCGAGAACGAGATCGTCAC
CGTCCACGGCTTTATCCGTTCCAAGTACAGGCTTAGGTTTCCAGAGCTCGAGTCGTTTGTGCATCACGCAATCGAGTACG
CTAGCGTCGTGAAACAAATCGGAGACGCTAAGGACCTAACCCTAGTCCCTCTCGAAGGTCTCTCAGCAAGTACCATCGAG
TACGCTAGCGTCGTGAAACAAATCGGAGATACTAAGGATCTAATAACCCAAGTCCCTCTCAAAGGTCTCTCAGCGCGTAC
AACTGTCTCTATTTTACTCACTGCTTCGACCACAAAGGGGAAGCCTCTGCCTTCAGATGTCTTGCAAAAGACGTTAGAGG
CGTGTGATCGAGCTATTGAGCTTGACTCCGCGCTGAAGAAGATTCTTGCCTTCGTTGAAACCAAGATGGGATGCATCGCA
CCGAATCTCTCAGCCGTTGTGGGGAGTGCTGTTGCAGCCAAGCTCATGGCTACTGCTGGAGGCTTGTCAGGGCTTGCTAA
GATGCCTTCATGTAACGTTCAAGTTCTTGGTCAGAAGAGGAAGAATCTTGACGGTTTCTCTGCTGTAACCACACAGTCTC
GTGTGGGTTACCTGGAGCATACTGAGATTTTCCAAAACACTCCTCCTGGACTTAGGAGCCGAGCTATCAAACTCTTGGCT
GGAAAGTCTACTTTGGCAGCTAGGGTTGACGCTTGTAGAGGAGACCCGTCGGGGACTAATGGTAGGTCTCTGAGGGAAGA
GATTCAGAAGAAGATTGATAAGTTGCAAGAGCCTGGTGTCGCAAGGCAGCCTAAGCCGCTTCCTGTTCCAGATATGACTT
CTAAGAAGAAGAGAGGTGGTCGGAGGCTAAGAAAGATGAAGGAAAGGTACGCGGTGACGGAGATGAGGAAGCTTTCCAAC
AGGGTGGCGTTTGGTGTAGCATGTGAAGAGAGCTCGCTTGGTGATGGGTTAGGTGAAGGGTATGGGATGCTTGGTCAGGG
TGGGAGCAAGAGGCTGCGAGTTTCCAGTGTTCCGAGCAAGCTGAAACTTGGTGCTAAGCTGGAAAAGAAGCTTAAAGAAA
GACAGTATACAAGTGGTGTTGCTACTACAGGCACTTCTGGTTTCATGACATCAAGACTTGCTTTCACTCCTGTGCAGGGA
ATAGAGCTGTGCAATCCTGGGGCTGTGAAATTATTTAGTGGGACTCAGAGCACTTACTTCTCAGAGTCAGGAACCTTCTC
CAAGATCAAGAAGATATAA

Alignment

ORF - retro_bole_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.02 %
• Parental protein coverage: 77.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIAIVHNFIRDKYRLKFQELESLVNHPIDYARVVKKIGNETDL-TLVDLEGLLPSAIIMVVSVTALTTKG
          E.A.V...I.D...L....LE.L....I.YA.VVK.IG...DL.T.V.L.GL...........TA.TTKG
Retrocopy EYASVVKQIGDAKDLTLVPLEGLSASTIEYASVVKQIGDTKDLITQVPLKGLSARTTVSIL-LTASTTKG

Parental  SPLPEDVLQKTLEACDRALELDSARKKVLDFVESKMGSIAPNLSAIVGSAVAAKLMGTAGGLSALAKMPA
          .PLP.DVLQKTLEACDRA.ELDSA.KK.L.FVE.KMG.IAPNLSA.VGSAVAAKLM.TAGGLS.LAKMP.
Retrocopy KPLPSDVLQKTLEACDRAIELDSALKKILAFVETKMGCIAPNLSAVVGSAVAAKLMATAGGLSGLAKMPS

Parental  CNVQVLGHKRKNLAGFSSATSQLRVGYLEQTEIFQSTPPALKSRAGRILAAKSTLAARVDATRGDPSGTN
          CNVQVLG.KRKNL.GFS..T.Q.RVGYLE.TEIFQ.TPP.L.SRA...LA.KSTLAARVDA.RGDPSGTN
Retrocopy CNVQVLGQKRKNLDGFSAVTTQSRVGYLEHTEIFQNTPPGLRSRAIKLLAGKSTLAARVDACRGDPSGTN

Parental  GKALREEIRKKIEKWQEPPPARQPKPLPVPDSEPKKRRGGRRLRKMKERYAVTDMRKLANRMAFGTP-EE
          G..LREEI.KKI.K.QEP..ARQPKPLPVPD...KK.RGGRRLRKMKERYAVT.MRKL.NR.AFG...EE
Retrocopy GRSLREEIQKKIDKLQEPGVARQPKPLPVPDMTSKKKRGGRRLRKMKERYAVTEMRKLSNRVAFGVACEE

Parental  SSLGDGLGEGYGMLGQAGSNRLRISSVPSKLKINPTIAKKLKERNYAGGATTSG----LTSSLAFTPVQG
          SSLGDGLGEGYGMLGQ.GS.RLR.SSVPSKLK......KKLKER.Y..G..T.G.....TS.LAFTPVQG
Retrocopy SSLGDGLGEGYGMLGQGGSKRLRVSSVPSKLKLGAKLEKKLKERQYTSGVATTGTSGFMTSRLAFTPVQG

Parental  IELCNPQQALGLGSGTQSTYFSESGTFSKLKKI
          IELCNP..A..L.SGTQSTYFSESGTFSK.KKI
Retrocopy IELCNP-GAVKLFSGTQSTYFSESGTFSKIKKI

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_6 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G60170	1 retrocopy	retro_atha_27,
Brassica oleracea	Bo1g091740	1 retrocopy	retro_bole_6 ,
Brassica rapa	Bra031522	1 retrocopy	retro_brap_23,
Solanum tuberosum	PGSC0003DMG400004771	1 retrocopy	retro_stub_45,