Basic Information
Gene Model:Bol034195
Gene Family:Not classificated
Chromosome:C03
Scaffold:Scaffold000039
Sequence:
 | 
Gene Structure
Nucleotide Length:6441 bp
Transcript Length:4443 bp
Protein Length:1480 aa
Strand:+
Location:C03: 1990978 : 1997418
Gene CDSs(9): 1-1139 | 1253-1867 | 2476-3493 | 3641-3911 | 4023-4147 | 4487-4950 | 5174-5202 | 5548-6189 | 6302-6441 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
ProfileScanPS50827DDT 306 366 14.994IPR018501DDT domain superfamily
ProfileScanPS50016ZF_PHD_2 502 549 10.015IPR019787Zinc finger, PHD-finger
Segsegseg 356 368 NANot foundNot found
Segsegseg 236 259 NANot foundNot found
Segsegseg 84 97 NANot foundNot found
HMMPfamPF00628PHD 1412 1463 5.4e-10IPR019787Zinc finger, PHD-finger
HMMPfamPF02178AT_hook 1347 1359 0.039IPR017956AT hook, DNA-binding motif
HMMPfamPF02178AT_hook 1254 1266 0.23IPR017956AT hook, DNA-binding motif
HMMPfamPF00628PHD 504 549 1.1e-16IPR019787Zinc finger, PHD-finger
HMMPfamPF02791DDT 309 366 0.0014IPR004022DDT domain
superfamilySSF57903FYVE/PHD zinc finger 1404 1479 4.1e-06IPR011011Zinc finger, FYVE/PHD-type
superfamilySSF57903FYVE/PHD zinc finger 1193 1250 0.00019IPR011011Zinc finger, FYVE/PHD-type
superfamilySSF57903FYVE/PHD zinc finger 496 565 1.9e-15IPR011011Zinc finger, FYVE/PHD-type
PatternScanPS01359ZF_PHD_1 505 546 NAIPR019786Zinc finger, PHD-type, conserved site
HMMSmartSM00249no description 1412 1461 0.037IPR001965Zinc finger, PHD-type
HMMSmartSM00384no description 1347 1359 0.37IPR017956AT hook, DNA-binding motif
HMMSmartSM00384no description 1254 1266 3.6IPR017956AT hook, DNA-binding motif
HMMSmartSM00109no description 1188 1239 0.039IPR002219Protein kinase C-like, phorbol ester/diacylglycerol binding
HMMSmartSM00109no description 494 543 0.21IPR002219Protein kinase C-like, phorbol ester/diacylglycerol binding
HMMSmartSM00249no description 504 547 7.1e-12IPR001965Zinc finger, PHD-type
HMMSmartSM00571no description 306 366 0.00026IPR018500DDT domain, subgroup
HMMPantherPTHR13712:SF22PHD ZINC FINGER-CONT 20 546 1.2e-09Not foundNot found
HMMPantherPTHR13712RING FINGER-CONTAINI 20 546 1.2e-09Not foundNot found
Gene3DG3DSA:3.30.40.10no description 1406 1469 8.4e-08Not foundNot found
Gene3DG3DSA:3.30.40.10no description 499 548 7.8e-12Not foundNot found
Gene Ontology
GO TermGO TypeDescription
GO:0003677 Molecular Function DNA binding
GO:0005515 Molecular Function protein binding
GO:0007242 Biological Process intracellular signaling cascade
GO:0008270 Molecular Function zinc ion binding
Swiss-Prot
Best HitE_value Description
Q128308e-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

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

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.oleraceaC03:1982512..4896037 (+)A.thalianaChr5:4002775..7686779 (+)386
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC03:1982512..3407547 (+)B.rapaA10:10299..1528392 (-)131
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
RAT5G1240040138134020909Chr5Subgenome_II626
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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