Basic Information
Gene Model:Bol027113
Gene Family:Not classificated
Chromosome:C07
Scaffold:Scaffold000078
Sequence:
 | 
Gene Structure
Nucleotide Length:4871 bp
Transcript Length:3279 bp
Protein Length:1092 aa
Strand:-
Location:C07: 161988 : 166858
Gene CDSs(17): 1-123 | 220-318 | 402-473 | 549-1119 | 1188-1300 | 1413-1512 | 1598-1720 | 1805-1872 | 1950-2102 | 2190-2333 | 2415-2633 | 2756-2840 | 2932-3083 | 3169-3318 | 3398-3451 | 3732-3860 | 3948-4871 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
HMMPfamPF00271Helicase_C 961 1039 1.2e-23IPR001650DNA/RNA helicase, C-terminal
HMMPfamPF00097zf-C3HC4 855 894 2.2e-14IPR018957Zinc finger, C3HC4 RING-type
HMMPfamPF00176SNF2_N 434 803 1.5e-61IPR000330SNF2-related
HMMPfamPF08797HIRAN 261 355 2.5e-17IPR014905HIP116, Rad5p N-terminal
Segsegseg 375 388 NANot foundNot found
PatternScanPS00518ZF_RING_1 870 879 NAIPR017907Zinc finger, RING-type, conserved site
superfamilySSF52540P-loop containing nu 907 1081 2.9e-24Not foundNot found
superfamilySSF52540P-loop containing nu 431 685 5e-21Not foundNot found
superfamilySSF57850RING/U-box 832 908 2.9e-15Not foundNot found
ProfileScanPS51194HELICASE_CTER 925 1087 15.638IPR001650DNA/RNA helicase, C-terminal
ProfileScanPS50089ZF_RING_2 855 895 12.371IPR001841Zinc finger, RING-type
ProfileScanPS51192HELICASE_ATP_BIND_1 489 686 19.425IPR014021Helicase, superfamily 1/2, ATP-binding domain
HMMSmartSM00184no description 855 894 5.6e-08IPR001841Zinc finger, RING-type
HMMSmartSM00490no description 956 1039 1.9e-19IPR001650DNA/RNA helicase, C-terminal
HMMSmartSM00487no description 427 703 1.9e-29IPR014001DEAD-like helicase, N-terminal
Gene3DG3DSA:3.30.40.10no description 848 909 2.9e-10Not foundNot found
Gene3DG3DSA:3.40.50.300no description 913 1079 5.5e-08Not foundNot found
HMMPantherPTHR10799ATP-DEPENDENT HELICA 2 1091 1.2e-255Not foundNot found
HMMPantherPTHR10799:SF62DNA REPAIR HELICASE 2 1091 1.2e-255Not 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
Q9FIY70.0SM3L3_ARATH Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 3 OS=Arabidopsis thaliana GN=At5g43530 PE=3 SV=1
TrEMBL
Best HitE_value Description
B9STJ20.0B9STJ2_RICCO DNA repair helicase rad5,16, putative OS=Ricinus communis GN=RCOM_0492090 PE=4 SV=1
KEGG
Best HitE_valueKOEC or Symbol Description
ssl:SS1G_032121e-136K01529E3.6.1.---
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.oleraceaC07:3570..599699 (-)A.thalianaChr5:17315449..17559354 (+)24
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC07:3570..656878 (+)B.rapaA06:22378908..22584739 (-)27
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
VAT5G435301748932717494830Chr5Subgenome_III(LF)22
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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