Basic Information
Gene Model:Bol026674
Gene Family:Not classificated
Chromosome:C03
Scaffold:Scaffold000082
Sequence:
 | 
Gene Structure
Nucleotide Length:4199 bp
Transcript Length:3003 bp
Protein Length:1000 aa
Strand:+
Location:C03: 23453447 : 23457645
Gene CDSs(10): 1-105 | 187-396 | 485-1030 | 1153-1371 | 1523-1584 | 1677-2619 | 2701-2778 | 2853-2924 | 3330-3988 | 4091-4199 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
HMMPfamPF00271Helicase_C 864 942 1.9e-21IPR001650DNA/RNA helicase, C-terminal
HMMPfamPF00097zf-C3HC4 710 747 9.3e-13IPR018957Zinc finger, C3HC4 RING-type
HMMPfamPF00176SNF2_N 279 621 1.6e-45IPR000330SNF2-related
Gene3DG3DSA:3.40.50.300no description 847 944 0.001Not foundNot found
Gene3DG3DSA:3.30.40.10no description 688 763 7.3e-12Not foundNot found
ProfileScanPS51194HELICASE_CTER 829 995 13.133IPR001650DNA/RNA helicase, C-terminal
ProfileScanPS51192HELICASE_ATP_BIND_1 291 580 12.578IPR014021Helicase, superfamily 1/2, ATP-binding domain
ProfileScanPS50089ZF_RING_2 710 749 11.442IPR001841Zinc finger, RING-type
PatternScanPS00518ZF_RING_1 725 734 NAIPR017907Zinc finger, RING-type, conserved site
superfamilySSF52540P-loop containing nu 845 974 2.4e-18Not foundNot found
superfamilySSF57850RING/U-box 685 754 4.4e-12Not foundNot found
superfamilySSF52540P-loop containing nu 236 582 9.8e-21Not foundNot found
HMMSmartSM00490no description 859 942 1.8e-17IPR001650DNA/RNA helicase, C-terminal
HMMSmartSM00184no description 710 748 4.2e-05IPR001841Zinc finger, RING-type
HMMSmartSM00487no description 272 595 9e-31IPR014001DEAD-like helicase, N-terminal
HMMPantherPTHR10799ATP-DEPENDENT HELICA 231 998 3.6e-239Not foundNot found
HMMPantherPTHR10799:SF62DNA REPAIR HELICASE 231 998 3.6e-239Not foundNot found
Segsegseg 487 507 NANot foundNot found
Segsegseg 775 793 NANot foundNot found
Segsegseg 470 479 NANot foundNot found
Segsegseg 336 347 NANot foundNot found
Segsegseg 83 96 NANot foundNot found
Segsegseg 8 18 NANot foundNot found
Gene Ontology
GO TermGO TypeDescription
GO:0003676 Molecular Function nucleic acid binding
GO:0003677 Molecular Function DNA binding
GO:0004386 Molecular Function helicase activity
GO:0005515 Molecular Function protein binding
GO:0005524 Molecular Function ATP binding
GO:0008270 Molecular Function zinc ion binding
Swiss-Prot
Best HitE_value Description
Q9FNI66e-92SM3L2_ARATH Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 2 OS=Arabidopsis thaliana GN=At5g22750 PE=2 SV=1
TrEMBL
Best HitE_value Description
Q9LHE40.0Q9LHE4_ARATH Transcription factor-like protein OS=Arabidopsis thaliana GN=At3g20010 PE=4 SV=1
KEGG
Best HitE_valueKOEC or Symbol Description

Note: this gene was not detected its best hit in KEGG database.

Gene Cluster
Orthologs
OrthoMCL GroupSpeciesGene List
ORTHOMCL339(32 genes,8 taxa):Arabidopsis thalianaAT1G11100.1
ORTHOMCL339(32 genes,8 taxa):Arabidopsis thalianaAT1G50410.1
ORTHOMCL339(32 genes,8 taxa):Arabidopsis thalianaAT1G61140.1
ORTHOMCL339(32 genes,8 taxa):Arabidopsis thalianaAT3G16600.1
ORTHOMCL339(32 genes,8 taxa):Arabidopsis thalianaAT3G20010.1
ORTHOMCL339(32 genes,8 taxa):Brassica oleraceaBol007356
ORTHOMCL339(32 genes,8 taxa):Brassica oleraceaBol010155
ORTHOMCL339(32 genes,8 taxa):Brassica oleraceaBol014069
ORTHOMCL339(32 genes,8 taxa):Brassica oleraceaBol018165
ORTHOMCL339(32 genes,8 taxa):Brassica oleraceaBol026674
ORTHOMCL339(32 genes,8 taxa):Brassica oleraceaBol035440
ORTHOMCL339(32 genes,8 taxa):Brassica rapaBra001771
ORTHOMCL339(32 genes,8 taxa):Brassica rapaBra018847
ORTHOMCL339(32 genes,8 taxa):Brassica rapaBra031452
ORTHOMCL339(32 genes,8 taxa):Brassica rapaBra035824
ORTHOMCL339(32 genes,8 taxa):Brassica rapaBra038573
ORTHOMCL339(32 genes,8 taxa):Vitis viniferaGSVIVT01006339001
ORTHOMCL339(32 genes,8 taxa):Vitis viniferaGSVIVT01034370001
ORTHOMCL339(32 genes,8 taxa):Oryza sativaOs01t0779400-01
ORTHOMCL339(32 genes,8 taxa):Oryza sativaOs01t0779400-02
ORTHOMCL339(32 genes,8 taxa):Oryza sativaOs04t0629300-01
ORTHOMCL339(32 genes,8 taxa):Oryza sativaOs04t0629300-02
ORTHOMCL339(32 genes,8 taxa):Oryza sativaOs08t0180300-01
ORTHOMCL339(32 genes,8 taxa):Oryza sativaOs08t0180300-02
ORTHOMCL339(32 genes,8 taxa):Oryza sativaOs08t0180300-03
ORTHOMCL339(32 genes,8 taxa):Populus trichocarpaPOPTR_0004s03790.1
ORTHOMCL339(32 genes,8 taxa):Populus trichocarpaPOPTR_0004s03790.2
ORTHOMCL339(32 genes,8 taxa):Populus trichocarpaPOPTR_0011s04620.1
ORTHOMCL339(32 genes,8 taxa):Sorghum bicolorSb03g036380.1
ORTHOMCL339(32 genes,8 taxa):Sorghum bicolorSb06g029476.1
ORTHOMCL339(32 genes,8 taxa):Sorghum bicolorSb07g005030.1
ORTHOMCL339(32 genes,8 taxa):Carica papayaevm.TU.supercontig_27.89
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.oleraceaC03:23215407..24458591 (+)A.thalianaChr3:6803072..7716343 (+)81
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC03:23393774..23928005 (+)B.rapaA05:6461983..7219016 (-)27
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
FAT3G2001069713526976595Chr3Subgenome_II468
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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