Basic Information
Gene Model:Bol044060
Gene Family:Not classificated
Chromosome:C09
Scaffold:Scaffold000004
Sequence:
 | 
Gene Structure
Nucleotide Length:2697 bp
Transcript Length:2547 bp
Protein Length:848 aa
Strand:-
Location:C09: 39222703 : 39225399
Gene CDSs(3): 1-809 | 892-1183 | 1252-2697 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
ProfileScanPS51192HELICASE_ATP_BIND_1 250 454 15.017IPR014021Helicase, superfamily 1/2, ATP-binding domain
ProfileScanPS51194HELICASE_CTER 678 843 15.314IPR001650DNA/RNA helicase, C-terminal
ProfileScanPS50089ZF_RING_2 603 642 12.563IPR001841Zinc finger, RING-type
HMMSmartSM00490no description 706 791 6.5e-16IPR001650DNA/RNA helicase, C-terminal
HMMSmartSM00487no description 205 461 5.2e-23IPR014001DEAD-like helicase, N-terminal
HMMSmartSM00184no description 603 641 8.8e-06IPR001841Zinc finger, RING-type
Segsegseg 652 666 NANot foundNot found
Segsegseg 17 28 NANot foundNot found
Segsegseg 296 311 NANot foundNot found
PatternScanPS00518ZF_RING_1 618 627 NAIPR017907Zinc finger, RING-type, conserved site
superfamilySSF57850RING/U-box 578 651 8.9e-16Not foundNot found
superfamilySSF52540P-loop containing nu 145 456 1.1e-16Not foundNot found
superfamilySSF52540P-loop containing nu 660 823 3e-24Not foundNot found
Gene3DG3DSA:3.40.50.300no description 679 831 4.6e-08Not foundNot found
Gene3DG3DSA:3.30.40.10no description 599 652 4.6e-12Not foundNot found
Coilcoilcoiled-coil 804 825 NANot foundNot found
HMMPfamPF00271Helicase_C 711 791 7e-21IPR001650DNA/RNA helicase, C-terminal
HMMPfamPF00176SNF2_N 212 560 1.5e-55IPR000330SNF2-related
HMMPfamPF00097zf-C3HC4 603 641 1.3e-10IPR018957Zinc finger, C3HC4 RING-type
HMMPfamPF08797HIRAN 36 133 1.4e-24IPR014905HIP116, Rad5p N-terminal
HMMPantherPTHR10799ATP-DEPENDENT HELICA 33 847 1.3e-279Not foundNot found
HMMPantherPTHR10799:SF61HELICASE SMARCA3 33 847 1.3e-279Not 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
Q9FF610.0SM3L1_ARATH Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 1 OS=Arabidopsis thaliana GN=At5g05130 PE=2 SV=1
TrEMBL
Best HitE_value Description
B9H8S60.0B9H8S6_POPTR Chromatin remodeling complex subunit (Fragment) OS=Populus trichocarpa GN=CHR931 PE=4 SV=1
KEGG
Best HitE_valueKOEC or Symbol Description
fgr:FG02724.12e-94K01529E3.6.1.---
Gene Cluster
Orthologs
OrthoMCL GroupSpeciesGene List
ORTHOMCL4086(12 genes,8 taxa):Arabidopsis thalianaAT5G05130.1
ORTHOMCL4086(12 genes,8 taxa):Brassica oleraceaBol044060
ORTHOMCL4086(12 genes,8 taxa):Brassica rapaBra009089
ORTHOMCL4086(12 genes,8 taxa):Vitis viniferaGSVIVT01025773001
ORTHOMCL4086(12 genes,8 taxa):Oryza sativaOs07t0642400-00
ORTHOMCL4086(12 genes,8 taxa):Populus trichocarpaPOPTR_0006s03420.1
ORTHOMCL4086(12 genes,8 taxa):Populus trichocarpaPOPTR_0016s03330.1
ORTHOMCL4086(12 genes,8 taxa):Populus trichocarpaPOPTR_0016s03350.1
ORTHOMCL4086(12 genes,8 taxa):Populus trichocarpaPOPTR_0311s00200.1
ORTHOMCL4086(12 genes,8 taxa):Populus trichocarpaPOPTR_0311s00210.1
ORTHOMCL4086(12 genes,8 taxa):Sorghum bicolorSb02g040960.1
ORTHOMCL4086(12 genes,8 taxa):Carica papayaevm.TU.supercontig_92.77
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.oleraceaC09:38329980..39305785 (-)A.thalianaChr5:1496855..2154553 (+)123
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC09:37411309..39260205 (+)B.rapaA10:2316765..3693243 (-)260
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
RAT5G0513015121201515079Chr5Subgenome_III(LF)638
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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