Basic Information
Gene Model:Bol030454
Gene Family:U-box Gene Family
Chromosome:C09
Scaffold:Scaffold000060
Sequence:
 | 
Gene Structure
Nucleotide Length:5101 bp
Transcript Length:3114 bp
Protein Length:1037 aa
Strand:+
Location:C09: 33424858 : 33429958
Gene CDSs(16): 1-177 | 263-352 | 451-615 | 696-788 | 870-992 | 1089-1184 | 1263-1466 | 1554-1643 | 1801-1915 | 2031-2143 | 2228-2431 | 2532-2684 | 2928-3192 | 3282-3433 | 3575-3779 | 4233-5101 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
HMMPantherPTHR13931:SF2UBIQUITINATION FACTO 67 1026 0Not foundNot found
HMMPantherPTHR13931UBIQUITINATION FACTO 67 1026 0Not foundNot found
Gene3DG3DSA:3.30.40.10no description 939 1013 1.1e-14Not foundNot found
Coilcoilcoiled-coil 518 546 NANot foundNot found
HMMPfamPF04564U-box 939 1013 2.1e-57IPR003613U box domain
HMMPfamPF10408Ufd2P_core 268 925 1.5e-275IPR019474Ubiquitin conjugation factor E4, core
superfamilySSF57850RING/U-box 944 999 1.5e-14Not foundNot found
HMMSmartSM00504no description 943 1006 7.2e-22IPR003613U box domain
Segsegseg 922 936 NANot foundNot found
Segsegseg 164 186 NANot foundNot found
Segsegseg 446 466 NANot foundNot found
Segsegseg 562 573 NANot foundNot found
Segsegseg 70 84 NANot 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.oleraceaC09:31552526..33899531 (-)A.thalianaChr5:4691006..6066186 (+)222
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC09:32272854..33899531 (+)B.rapaA10:10299..911027 (+)162
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
RAT5G1540049976115003140Chr5Subgenome_III(LF)389
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


logo