RetrogeneDB ID: retro_bole_31

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C4:11673277..11674597(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo4g052020
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo1g008280
• Aliases: None
• Description: None

Sequence

>retro_bole_31
ATGAATGCAGGTATGAACTGGAAGGAACATGGTCGGAAGATTCCCAAGGAAAATCTGGACAGATTCATACCGAACAGATC
AGCTATGGATTTCGACTTTGCTCATCACGCCCTCACCGAAGCCCTAATCGAAGCAAGAGACGGCCAAAAAAAAGAAGCGC
GGGAGCTTTCACCCTCCAAAGAGGCTTACAGGAAGCGTTTGGCTGAAACGCTCGGTCTCAACCGCACCCGTATTCTCGCC
TTCAGGAACAAACCTCAACCTCCTCTCCACTCTCATTATCACTCTGCTTCTCTTCACCAACAACCTCTAAAGCCTCGCCG
CCGACGCATTCCTCAGTCTTGTAGCAGAGTCTTGGATGCTCCTAACATTCTTGACGACTTCTACCTCAACTTGCTTGACT
GGGGTTCTCGTAACGTCTTAGCTATTGCCTTGGGCCACACTCTTTGCCTCTGGGATGCTTCTACCGGCTCTGTATCCGAG
TTCGTGACCATTGAGGAAGACCAAGGACCCATCACAAGCATAAGCTGGGCACCTGATGGTTCCCACGTTGCACTTGGCCT
CAACAACTCTCAAGTCCAGCTTTGGGATTCTTCATCCATCCGCAAGATAAGAACTTTGAACGGTGTCCACCACTCTAGAG
TAGGATCACTTGCATGGAACAATCACATCCTCACAACCGGAGGAATGGACGGGAAGATTGTCAACAACGATGTCAGGATC
AGGTCGCATGTTGTGGGAACTTACAGAGGTCACACTGGAGAGATTTGTGGACTCAAGTGGTCAGGTTCTGGAATGCAGCT
TGCTAGTGGTGGCAACGATAATGTGGTTCACGTATGGGATCTCTCTTCTGCGTCTTCGAGATGGCTGCACAGGCTTGAGG
AACATACTTCTGCCGTGAAAGCTCTTGCTTGGTGCCCCTTCCAATCGAATTTGCTTGCAACTGGTGGTGGTGGAACAGAT
GGGGCGATCAAGTTCTGGAACACTCACACCGGAGCTTGCTTGAACTCTGTAGACACAGGATCCCAAGTGTGTGCTTTGTT
GTGGAGCAAGAATGACAGAGAGTTGCTTAGCTCACATGGGTTTTCTCAGAACCACCTTGCACTTTGGAAGTACCCATCCT
TGGTGAAAATGGCTGAGCTCACTGGCCATACATCAAGAGTTCTGTATATGACACAGAGTCCTGATGGCTCTACCGTTGCT
TCAGCTGCAGGAGACGAGAGTTTGAGGTTTTGGGATGTTTTTGGAATGCCAGAGACTGCCAAAAAACCTGTTCAGAAAGC
AGCCCATGAGCCATTTTCTCGCGTGCCTCGTATCCGTTGA

Alignment

ORF - retro_bole_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.06 %
• Parental protein coverage: 94.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKSSKENLDRFIPNRSAMDFDYAHYALT----EGRNGKDQATAAVSSPSREAYRKQLAETMNLNHTRILA
          RK..KENLDRFIPNRSAMDFD.AH.ALT....E.R.G........S.PS.EAYRK.LAET..LN.TRILA
Retrocopy RKIPKENLDRFIPNRSAMDFDFAHHALTEALIEARDGQKKEARELS-PSKEAYRKRLAETLGLNRTRILA

Parental  FRNKPQAPVELLPTDHSASLHQQPRSVKPRRYIPQTSERTLDAPDIVDDFYLNLLDWGSANVLAIALGHT
          FRNKPQ.P..L....HSASLHQQP.....RR.IPQ...R.LDAP.I.DDFYLNLLDWGS.NVLAIALGHT
Retrocopy FRNKPQPP--LHSHYHSASLHQQPLKPRRRR-IPQSCSRVLDAPNILDDFYLNLLDWGSRNVLAIALGHT

Parental  VYLWDASSGSTSELVTIDEEKGPVTSINWAPDGRHVAVGLNNSEVQLWDSASNRQLRTLKGGHQSRVGSM
          ..LWDAS.GS.SE.VTI.E..GP.TSI.WAPDG.HVA.GLNNS.VQLWDS.S.R..RTL.G.H.SRVGS.
Retrocopy LCLWDASTGSVSEFVTIEEDQGPITSISWAPDGSHVALGLNNSQVQLWDSSSIRKIRTLNGVHHSRVGSL

Parental  AWNNHILTTGGMDGQIVNNDVRIRSHVVETYRGHTQEVCGLKWSGSGQQLASGGNDNVVHIWDRSVASSN
          AWNNHILTTGGMDG.IVNNDVRIRSHVV.TYRGHT.E.CGLKWSGSG.QLASGGNDNVVH.WD.S.ASS.
Retrocopy AWNNHILTTGGMDGKIVNNDVRIRSHVVGTYRGHTGEICGLKWSGSGMQLASGGNDNVVHVWDLSSASS-

Parental  STTQYLHRLEEHTSAVKALAWCPFQANLLATGGGGGDRTIKFWNTHTGACLNSVDTGSQVCSLLWSKNER
          .....LHRLEEHTSAVKALAWCPFQ.NLLATGGGG.D..IKFWNTHTGACLNSVDTGSQVC.LLWSKN.R
Retrocopy ---RWLHRLEEHTSAVKALAWCPFQSNLLATGGGGTDGAIKFWNTHTGACLNSVDTGSQVCALLWSKNDR

Parental  ELLSSHGFTQNQLTLWKYPSMVKMAELTGHTSRVLYMAQSPDGCTVATAAGDETLRFWNVFGVPETAKKA
          ELLSSHGF.QN.L.LWKYPS.VKMAELTGHTSRVLYM.QSPDG.TVA.AAGDE.LRFW.VFG.PETAKK.
Retrocopy ELLSSHGFSQNHLALWKYPSLVKMAELTGHTSRVLYMTQSPDGSTVASAAGDESLRFWDVFGMPETAKKP

Parental  APKAAHEPFSHVNRIR
          ..KAAHEPFS.V.RIR
Retrocopy VQKAAHEPFSRVPRIR

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_31 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo1g008280	1 retrocopy	retro_bole_31 ,
Arabidopsis lyrata	fgenesh2_kg.7__793__AT4G33270.1	1 retrocopy	retro_alyr_4,