Basic Information
Gene Model:Bol043497
Gene Family:Not classificated
Chromosome:C09
Scaffold:Scaffold000004
Sequence:
 | 
Gene Structure
Nucleotide Length:6708 bp
Transcript Length:4836 bp
Protein Length:1611 aa
Strand:-
Location:C09: 35905430 : 35912137
Gene CDSs(10): 1-130 | 195-303 | 407-1042 | 1343-1371 | 1590-2071 | 2366-2493 | 2591-2882 | 3214-4105 | 4469-4972 | 5075-6708 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
ProfileScanPS50827DDT 471 531 16.469IPR018501DDT domain superfamily
ProfileScanPS50016ZF_PHD_2 630 677 9.632IPR019787Zinc finger, PHD-finger
Gene3DG3DSA:3.30.40.10no description 606 676 9.1e-15Not foundNot found
Gene3DG3DSA:3.30.40.10no description 1504 1567 3.3e-07Not foundNot found
HMMPantherPTHR13712:SF22PHD ZINC FINGER-CONT 64 674 5.2e-08Not foundNot found
HMMPantherPTHR13712RING FINGER-CONTAINI 64 674 5.2e-08Not foundNot found
superfamilySSF57903FYVE/PHD zinc finger 1502 1577 4.1e-06IPR011011Zinc finger, FYVE/PHD-type
superfamilySSF57903FYVE/PHD zinc finger 624 693 1.4e-16IPR011011Zinc finger, FYVE/PHD-type
PatternScanPS01359ZF_PHD_1 602 674 NAIPR019786Zinc finger, PHD-type, conserved site
HMMSmartSM00249no description 1510 1559 0.0034IPR001965Zinc finger, PHD-type
HMMSmartSM00571no description 471 531 9.8e-09IPR018500DDT domain, subgroup
HMMSmartSM00249no description 632 675 3.2e-13IPR001965Zinc finger, PHD-type
Segsegseg 452 473 NANot foundNot found
Segsegseg 1595 1607 NANot foundNot found
HMMPfamPF00628PHD 1510 1561 1.7e-10IPR019787Zinc finger, PHD-finger
HMMPfamPF02791DDT 474 531 1.5e-05IPR004022DDT domain
HMMPfamPF00628PHD 632 677 1.5e-16IPR019787Zinc finger, PHD-finger
Gene Ontology
GO TermGO TypeDescription
GO:0005515 Molecular Function protein binding
GO:0008270 Molecular Function zinc ion binding
Swiss-Prot
Best HitE_value Description
Q128303e-18BPTF_HUMAN Nucleosome-remodeling factor subunit BPTF OS=Homo sapiens GN=BPTF PE=1 SV=3
TrEMBL
Best HitE_value Description
Q94CK20.0Q94CK2_ARATH Putative uncharacterized protein At5g12400 OS=Arabidopsis thaliana GN=At5g12400 PE=2 SV=1
KEGG
Best HitE_valueKOEC or Symbol Description
tca:1001417902e-20K11728BPTF, E(bx)nucleosome-remodeling factor subunit BPTF
Gene Cluster
Orthologs
OrthoMCL GroupSpeciesGene List
ORTHOMCL5225(11 genes,6 taxa):Arabidopsis thalianaAT5G12400.1
ORTHOMCL5225(11 genes,6 taxa):Brassica oleraceaBol003554
ORTHOMCL5225(11 genes,6 taxa):Brassica oleraceaBol034195
ORTHOMCL5225(11 genes,6 taxa):Brassica oleraceaBol043497
ORTHOMCL5225(11 genes,6 taxa):Brassica rapaBra006158
ORTHOMCL5225(11 genes,6 taxa):Brassica rapaBra008890
ORTHOMCL5225(11 genes,6 taxa):Brassica rapaBra023376
ORTHOMCL5225(11 genes,6 taxa):Vitis viniferaGSVIVT01037231001
ORTHOMCL5225(11 genes,6 taxa):Populus trichocarpaPOPTR_0001s26130.1
ORTHOMCL5225(11 genes,6 taxa):Populus trichocarpaPOPTR_0009s05370.1
ORTHOMCL5225(11 genes,6 taxa):Sorghum bicolorSb02g042000.1
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.oleraceaC09:34943029..37985607 (-)A.thalianaChr5:2455634..4703084 (+)379
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC09:34943029..37404597 (+)B.rapaA10:897866..2370845 (+)281
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
RAT5G1240040138134020909Chr5Subgenome_III(LF)638
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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