Basic Information
Gene Model:Bol021231
Gene Family:U-box Gene Family
Chromosome:C02
Scaffold:Scaffold000116
Sequence:
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Gene Structure
Nucleotide Length:4929 bp
Transcript Length:3126 bp
Protein Length:1041 aa
Strand:-
Location:C02: 3528313 : 3533241
Gene CDSs(15): 1-174 | 256-345 | 427-591 | 668-760 | 845-1063 | 1141-1344 | 1434-1523 | 1639-1753 | 1856-1968 | 2049-2252 | 2352-2504 | 2752-3019 | 3111-3262 | 3435-3639 | 4049-4929 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
superfamilySSF57850RING/U-box 949 1004 9.2e-15Not foundNot found
Segsegseg 567 578 NANot foundNot found
Segsegseg 927 941 NANot foundNot found
Segsegseg 450 469 NANot foundNot found
Segsegseg 25 35 NANot foundNot found
HMMPantherPTHR13931UBIQUITINATION FACTO 7 1030 0Not foundNot found
HMMPantherPTHR13931:SF2UBIQUITINATION FACTO 7 1030 0Not foundNot found
HMMSmartSM00504no description 948 1011 2.8e-23IPR003613U box domain
HMMPfamPF10408Ufd2P_core 272 930 3.4e-274IPR019474Ubiquitin conjugation factor E4, core
HMMPfamPF04564U-box 944 1018 1.5e-58IPR003613U box domain
Coilcoilcoiled-coil 523 551 NANot foundNot found
Gene3DG3DSA:3.30.40.10no description 944 1018 9.6e-15Not foundNot found
Gene Ontology
GO TermGO TypeDescription
GO:0000151 Cellular Component ubiquitin ligase complex
GO:0004842 Molecular Function ubiquitin-protein ligase activity
GO:0005515 Molecular Function protein binding
GO:0006511 Biological Process ubiquitin-dependent protein catabolic process
GO:0016567 Biological Process protein ubiquitination
GO:0034450 Molecular Function ubiquitin-ubiquitin ligase activity
Swiss-Prot
Best HitE_value Description
Q9LF410.0UBE4_ARATH Probable ubiquitin conjugation factor E4 OS=Arabidopsis thaliana GN=PUB1 PE=1 SV=1
TrEMBL
Best HitE_value Description
B9T3S80.0B9T3S8_RICCO Ubiquitin-protein ligase, putative OS=Ricinus communis GN=RCOM_0169100 PE=4 SV=1
KEGG
Best HitE_valueKOEC or Symbol Description
ath:AT5G154000.0K10597UBE4B, UFD2ubiquitin conjugation factor E4 B
Gene Cluster
Orthologs
OrthoMCL GroupSpeciesGene List
ORTHOMCL5245(11 genes,8 taxa):Arabidopsis thalianaAT5G15400.1
ORTHOMCL5245(11 genes,8 taxa):Brassica oleraceaBol021231
ORTHOMCL5245(11 genes,8 taxa):Brassica oleraceaBol030454
ORTHOMCL5245(11 genes,8 taxa):Brassica rapaBra008700
ORTHOMCL5245(11 genes,8 taxa):Brassica rapaBra023516
ORTHOMCL5245(11 genes,8 taxa):Vitis viniferaGSVIVT01011484001
ORTHOMCL5245(11 genes,8 taxa):Oryza sativaOs03t0427900-01
ORTHOMCL5245(11 genes,8 taxa):Populus trichocarpaPOPTR_0004s12060.1
ORTHOMCL5245(11 genes,8 taxa):Populus trichocarpaPOPTR_0017s12530.1
ORTHOMCL5245(11 genes,8 taxa):Sorghum bicolorSb01g032170.1
ORTHOMCL5245(11 genes,8 taxa):Carica papayaevm.TU.supercontig_14.139
Tandem Duplication
ClusterGene Num.Gene List

The tandem genes of this gene was not detected with strict parameters, so there is no information collected in Bolbase.

Synteny Analysis
Synteny Genes
Compared to A.thaliana Compared to B.rapa
Synteny Regions
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC02:3260082..5447020 (+)A.thalianaChr5:4729319..6673282 (+)218
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC02:3260082..4171696 (+)B.rapaA10:10299..881157 (-)82
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
RAT5G1540049976115003140Chr5Subgenome_I556
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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