RetrogeneDB ID: retro_bole_26

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C7:29501931..29504013(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo7g078150
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo8g104580
• Aliases: None
• Description: None

Sequence

>retro_bole_26
ATGAACAAAATACAATCGATGGCTAGTGTCCAGCAAAACAGACAAATTAGATACGGTATTACAGAACCTATCTCTCTAGG
AGGACCAACGGAGCTTGACGTAATCAAGACAAAAGCCCTAGAGAACTACTTGCAAGACGCTGGATTATACGAAAGCAACG
AGGAAGCTCTTAGAAGAGAGGAGGTTCTTGGGAGACTAGACGAGATCGTAAAAACATGGATTAAAAAAATAAGCCGTGAC
AAAGGGTTAAGCGATGAGACGGTTGAACAAGCGAACGCCAAGATATTCACCTTCGGTTCTTATCGGCTAAAGGTACATGG
ACCTGGTGCTGATATCGACACTCTATGCGTTGGTCCAAGATACGCAACAAGAGGGAATGGTTTCTTTGGAGAGCTACACA
GAATGCTTTCGGAGTTGCCTGAAGTGACAGAGCTCCACTCTGTCCCTGATGCTTATGTTCCCTTGATGGGTTTCAAACTT
AATGGAGTCTCTATTGATCTCCTCTACGCAAAGCTTCCTCTATGGATTATCCCTGAAGACTTGGATCTATCAGATGATTC
AATTCTACAGAATGCTGATGAGCAAACTGTTAGAAGCCTCAACGGTTGTAGAGTTACAGACAAGATCTTCCGCTTGGTTC
CTAACATTCAGAGTTTCAGGACGACGTTAAGATGCATTAGGTTTTGGGCCAAGAAGCGTGGTGTGTACTCTAACGTCTCT
GGCTTTCTTGGTGGTATAAACTGGGCGTTGCTTGTAGCTAGAATCTGTCAGCTTTATCCTAACGCATCACCAAACATGTT
GGTGTCTCGGTTCTTTAGAGTCTACACGCAATGGCGTTGGCCCAATCCCATCCTTCTTTGCTCTATCGATGAAGAAGGTT
CCTCCTCCTTAGGTCTTCAAGTTTGGGATCCTAGAAGAAACCCTAAAGACTTGTTGCACAAGATGCCTATCATTACTCCT
GCTTATCCTTGTATGAACTCTAGTTACAATGTCTCCGCGAGTACACTGAGGATTATGACAGGAGAGTTTCAGAGAGGTAA
AGATATATGCGCGGCTATGGAAGGAAACGAAGCTGATCAATGGGATACACTTTTTGAGCCGTTTGGGTTCTTTGAAGCGT
ATAAGAACTATCTTCAGATCAACATCTCTGCTTCTAACGTGGAGGATCTGAAAAAGTGGAGAGGATGGGTTGAGTCACGT
TTCAGACAGCTGACGTTGGTGATTGAGAGACATACTTGTGACATGCTTCAGTGCCACCCTCATCCACATGGTTTCCAAGA
TGATTCAAAACCGCTACAGTGTTCTTTATTCATGGGTCTGCAACGTAAACAAGGAGTTACAGCAGTAGGAGGAGAACCGT
TTGATATCAGAAGAACTATTGAGGAGTTTAAACAAACTGTTTACGGTTACACGTTGTGGTCTCCTAGGATGGAGATTAAT
GTTAGCCATGTAATGCGAAGAAGCATACCTAGCTTTGTGTTTCCTGGTGGAGTTAGACCTTTGCGTAACTCGAAAGGAAC
TTGGGACAGCAAACGCAGTTCAGAGCAGAGAGTTTCTTCTACAGGGAGTTCATCATCTACTATTACTAGTTGTGAAAGTA
AAGGTGGGAAGAAGAGAAAGTTGGGAGATGATGAGACATTCACCGATCAGTTAAGGAACTCAAAACGTGTTGCAGTTTCA
GTGCATGTAGAGAACGGCGAAGATGGGAGTCCAAATTCATCTGTTGAATCCATTTGTTCAGCTCCTATGAAAGAACTTTG
TACTAAGGTTGAATATGATCCCATCAGTAAGGGTGTAGGAGAGAGTCATCCAGTAGAGAAGATAGCCACTCCTCAGGCTT
CTCTTAGTCAAGAAAGTGAGGAAGTTGAAGACAACTTTGGCTTCAGAAATCAAGTGGTTAAGCAAATTCCAAGTAAAGAT
GCATTCTCCAAAGGAGCAGTGGAAGTGGAAGAACTCGAAGATGTTCCAACGCAACAGTCAGTGGTGACGCATAAAGCTTC
AGTGCAACTGCAGAAGCCGATAATCAAGTTGAATTTCACATCTCTAAGCACAATCAATGCCAAGAACCTCAGAGCTTATT
GA

Alignment

ORF - retro_bole_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.44 %
• Parental protein coverage: 73.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASVQQNGQ-RYGITEPISLGGPTELDVVKTRELEKYLQDVGLYESKEEAVRREEVLGRLDQIVKTWIKT
          MASVQQN.Q.RYGITEPISLGGPTELDV.KT..LE.YLQD.GLYES.EEA.RREEVLGRLD.IVKTWIK.
Retrocopy MASVQQNRQIRYGITEPISLGGPTELDVIKTKALENYLQDAGLYESNEEALRREEVLGRLDEIVKTWIKK

Parental  ISRAKGLNDQLLHEANAEIFTFGSYRLGVHGPGADIDTLCVGPRHATREGDFFGELQRMLSEMPEVTELH
          ISR.KGL.D.....ANA.IFTFGSYRL.VHGPGADIDTLCVGPR.ATR...FFGEL.RMLSE.PEVTELH
Retrocopy ISRDKGLSDETVEQANAKIFTFGSYRLKVHGPGADIDTLCVGPRYATRGNGFFGELHRMLSELPEVTELH

Parental  PVPDAHVPLMGFKLNGVSIDLLYAQLPLWVIPKDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPNI
          .VPDA.VPLMGFKLNGVSIDLLYA.LPLW.IP.DLD.S.DSILQNADEQTVRSLNGCRVTD.I.RLVPNI
Retrocopy SVPDAYVPLMGFKLNGVSIDLLYAKLPLWIIPEDLDLSDDSILQNADEQTVRSLNGCRVTDKIFRLVPNI

Parental  ENFRTTLRCMRFWAKRRGVYSNVSGFLGGINWALLVARICQLYPNALPNMLASRFFRVYTQWRWPNPVLL
          ..FRTTLRC.RFWAK.RGVYSNVSGFLGGINWALLVARICQLYPNA.PNML.SRFFRVYTQWRWPNP.LL
Retrocopy QSFRTTLRCIRFWAKKRGVYSNVSGFLGGINWALLVARICQLYPNASPNMLVSRFFRVYTQWRWPNPILL

Parental  CSMDE---GSLGLQVWDPRRNPKDRLHMMPIITPAYPCMNSSYNVSASTLRIMTGEFQRGKDICEAMEAN
          CS.DE....SLGLQVWDPRRNPKD.LH.MPIITPAYPCMNSSYNVSASTLRIMTGEFQRGKDIC.AME.N
Retrocopy CSIDEEGSSSLGLQVWDPRRNPKDLLHKMPIITPAYPCMNSSYNVSASTLRIMTGEFQRGKDICAAMEGN

Parental  KAD-WDTLFEPFAFFEAYKNYLQIDISAANVDDLRKWKGWVESRLRQLTLKIERHTYDMLQCHPHPHDFQ
          .AD.WDTLFEPF.FFEAYKNYLQI.ISA.NV.DL.KW.GWVESR.RQLTL.IERHT.DMLQCHPHPH.FQ
Retrocopy EADQWDTLFEPFGFFEAYKNYLQINISASNVEDLKKWRGWVESRFRQLTLVIERHTCDMLQCHPHPHGFQ

Parental  DASRPLHCSYFMGLQRKQGVPAAEGEPFDIRRTVEEFKHTVNGYMLWIPGMEISVSHIKRRSLPSFVFPG
          D.S.PL.CS.FMGLQRKQGV.A..GEPFDIRRT.EEFK.TV.GY.LW.P.MEI.VSH..RRS.PSFVFPG
Retrocopy DDSKPLQCSLFMGLQRKQGVTAVGGEPFDIRRTIEEFKQTVYGYTLWSPRMEINVSHVMRRSIPSFVFPG

Parental  GVRPSHASKGTWDSKRRAEHRVSSTASAATTTTA
          GVRP...SKGTWDSKR..E.RVSST.S...T.T.
Retrocopy GVRPLRNSKGTWDSKRSSEQRVSSTGSSSSTITS

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_26 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g104580	1 retrocopy	retro_bole_26 ,
Brassica rapa	Bra031010	1 retrocopy	retro_brap_15,
Triticum aestivum	Traes_4AL_4A747B462	1 retrocopy	retro_taes_53,