Basic Information
Gene Model:Bol025846
Gene Family:Not classificated
Chromosome:C03
Scaffold:Scaffold000085
Sequence:
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Gene Structure
Nucleotide Length:4823 bp
Transcript Length:3075 bp
Protein Length:1024 aa
Strand:-
Location:C03: 4817784 : 4822606
Gene CDSs(20): 1-123 | 214-312 | 403-474 | 577-670 | 758-958 | 1040-1321 | 1415-1527 | 1586-1685 | 1763-1885 | 1979-2046 | 2189-2344 | 2450-2596 | 2692-2961 | 3046-3130 | 3208-3359 | 3433-3573 | 3662-3715 | 3874-4009 | 4087-4220 | 4299-4823 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
ProfileScanPS51194HELICASE_CTER 859 1024 15.090IPR001650DNA/RNA helicase, C-terminal
ProfileScanPS51192HELICASE_ATP_BIND_1 400 616 20.783IPR014021Helicase, superfamily 1/2, ATP-binding domain
ProfileScanPS50089ZF_RING_2 789 829 12.917IPR001841Zinc finger, RING-type
HMMPantherPTHR10799ATP-DEPENDENT HELICA 113 1024 4.5e-266Not foundNot found
HMMPantherPTHR10799:SF62DNA REPAIR HELICASE 113 1024 4.5e-266Not foundNot found
Gene3DG3DSA:3.40.50.300no description 859 1011 2.8e-05Not foundNot found
Gene3DG3DSA:3.30.40.10no description 785 839 1.8e-13Not foundNot found
Segsegseg 290 301 NANot foundNot found
Segsegseg 250 262 NANot foundNot found
Segsegseg 53 68 NANot foundNot found
Segsegseg 92 104 NANot foundNot found
PatternScanPS00518ZF_RING_1 804 813 NAIPR017907Zinc finger, RING-type, conserved site
HMMSmartSM00490no description 888 971 6e-18IPR001650DNA/RNA helicase, C-terminal
HMMSmartSM00487no description 338 635 6.6e-27IPR014001DEAD-like helicase, N-terminal
HMMSmartSM00184no description 789 828 6.2e-09IPR001841Zinc finger, RING-type
HMMPfamPF00271Helicase_C 893 971 1.6e-22IPR001650DNA/RNA helicase, C-terminal
HMMPfamPF00097zf-C3HC4 789 828 1.5e-15IPR018957Zinc finger, C3HC4 RING-type
HMMPfamPF08797HIRAN 109 222 5e-27IPR014905HIP116, Rad5p N-terminal
HMMPfamPF00176SNF2_N 345 733 2.8e-64IPR000330SNF2-related
superfamilySSF57850RING/U-box 764 842 5.8e-17Not foundNot found
superfamilySSF52540P-loop containing nu 302 615 3.3e-21Not foundNot found
superfamilySSF52540P-loop containing nu 839 1013 8.7e-23Not 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
GO:0016818 Molecular Function hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Swiss-Prot
Best HitE_value Description
Q9FNI60.0SM3L2_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
B9SN700.0B9SN70_RICCO DNA repair helicase rad5,16, putative OS=Ricinus communis GN=RCOM_1186120 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
ORTHOMCL1864(16 genes,8 taxa):Arabidopsis thalianaAT5G22750.1
ORTHOMCL1864(16 genes,8 taxa):Arabidopsis thalianaAT5G43530.1
ORTHOMCL1864(16 genes,8 taxa):Brassica oleraceaBol025846
ORTHOMCL1864(16 genes,8 taxa):Brassica oleraceaBol027113
ORTHOMCL1864(16 genes,8 taxa):Brassica rapaBra006634
ORTHOMCL1864(16 genes,8 taxa):Brassica rapaBra033682
ORTHOMCL1864(16 genes,8 taxa):Vitis viniferaGSVIVT01027728001
ORTHOMCL1864(16 genes,8 taxa):Vitis viniferaGSVIVT01031410001
ORTHOMCL1864(16 genes,8 taxa):Oryza sativaOs02t0527100-01
ORTHOMCL1864(16 genes,8 taxa):Oryza sativaOs04t0177300-01
ORTHOMCL1864(16 genes,8 taxa):Populus trichocarpaPOPTR_0003s08160.1
ORTHOMCL1864(16 genes,8 taxa):Populus trichocarpaPOPTR_0004s20080.1
ORTHOMCL1864(16 genes,8 taxa):Sorghum bicolorSb04g021470.1
ORTHOMCL1864(16 genes,8 taxa):Sorghum bicolorSb06g003030.1
ORTHOMCL1864(16 genes,8 taxa):Carica papayaevm.TU.supercontig_44.83
ORTHOMCL1864(16 genes,8 taxa):Carica papayaevm.TU.supercontig_47.56
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.oleraceaC03:1982512..4896037 (+)A.thalianaChr5:4002775..7686779 (+)386
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC03:3384356..7484156 (+)B.rapaA10:5981599..12607476 (+)333
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block

Note: this gene was no corresponding triplicated genes.

 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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