Basic Information
Gene Model:Bol044486
Gene Family:Transcription Factor Families
Chromosome:C08
Scaffold:Scaffold000002
Sequence:
 | 
Gene Structure
Nucleotide Length:6778 bp
Transcript Length:2703 bp
Protein Length:900 aa
Strand:-
Location:C08: 31590046 : 31596823
Gene CDSs(10): 1-59 | 453-853 | 1287-1385 | 1468-1592 | 1667-2206 | 2333-2644 | 5224-5574 | 5720-5785 | 5910-6633 | 6753-6778 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
Gene3DG3DSA:4.10.280.10no description 237 295 3.5e-09IPR011598Helix-loop-helix DNA-binding
HMMSmartSM00353no description 246 295 4.8e-18IPR001092Basic helix-loop-helix dimerisation region bHLH
superfamilySSF47459HLH, helix-loop-heli 236 314 2.7e-19IPR011598Helix-loop-helix DNA-binding
superfamilySSF48452TPR-like 80 814 2.4e-23Not foundNot found
HMMPantherPTHR10483PENTATRICOPEPTIDE RE 484 883 2.1e-108Not foundNot found
HMMPfamPF01535PPR 824 858 6.3e-06IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 789 823 2.7e-12IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 754 788 3.8e-10IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 719 753 3.6e-07IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 684 718 5.5e-11IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 663 683 0.0025IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 617 651 1e-05IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 544 578 8.3e-09IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 579 613 0.0016IPR002885Pentatricopeptide repeat
HMMPfamPF01535PPR 514 543 0.00057IPR002885Pentatricopeptide repeat
HMMPfamPF00010HLH 241 290 1.7e-17IPR001092Basic helix-loop-helix dimerisation region bHLH
Segsegseg 303 310 NANot foundNot found
Segsegseg 326 341 NANot foundNot found
Segsegseg 617 628 NANot foundNot found
Segsegseg 250 255 NANot foundNot found
Segsegseg 229 240 NANot foundNot found
Segsegseg 110 131 NANot foundNot found
Segsegseg 89 100 NANot foundNot found
Coilcoilcoiled-coil 246 267 NANot foundNot found
ProfileScanPS51375PPR 822 856 9.383IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 787 821 12.485IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 752 786 11.049IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 682 716 13.340IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 717 751 10.117IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 615 649 10.665IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 577 611 9.909IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 507 541 8.374IPR002885Pentatricopeptide repeat
ProfileScanPS51375PPR 542 576 11.696IPR002885Pentatricopeptide repeat
ProfileScanPS50888HLH 237 290 16.617IPR001092Basic helix-loop-helix dimerisation region bHLH
HMMTigrTIGR00756PPR: pentatricopepti 789 823 2.8e-10IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 824 858 2.2e-05IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 754 788 5.4e-08IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 684 718 2.2e-09IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 719 753 2.2e-06IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 652 683 0.045IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 579 613 0.0021IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 617 651 2.5e-06IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 509 543 0.0052IPR002885Pentatricopeptide repeat
HMMTigrTIGR00756PPR: pentatricopepti 544 578 4.7e-07IPR002885Pentatricopeptide repeat
Gene Ontology
GO TermGO TypeDescription
GO:0005634 Cellular Component nucleus
GO:0030528 Molecular Function transcription regulator activity
GO:0045449 Biological Process regulation of transcription
Swiss-Prot
Best HitE_value Description
Q9LYT20.0PP287_ARATH Pentatricopeptide repeat-containing protein At3g59040 OS=Arabidopsis thaliana GN=At3g59040 PE=2 SV=2
TrEMBL
Best HitE_value Description
Q3EAH80.0Q3EAH8_ARATH Putative uncharacterized protein At3g59040.2 OS=Arabidopsis thaliana GN=At3g59040 PE=4 SV=1
KEGG
Best HitE_valueKOEC or Symbol Description
ath:AT1G095301e-25K12126PIF3phytochrome-interacting factor 3
Gene Cluster
Orthologs
OrthoMCL GroupSpeciesGene List
ORTHOMCL10040(8 genes,8 taxa):Arabidopsis thalianaAT3G59040.2
ORTHOMCL10040(8 genes,8 taxa):Brassica oleraceaBol044486
ORTHOMCL10040(8 genes,8 taxa):Brassica rapaBra007430
ORTHOMCL10040(8 genes,8 taxa):Vitis viniferaGSVIVT01020809001
ORTHOMCL10040(8 genes,8 taxa):Oryza sativaOs08t0191900-01
ORTHOMCL10040(8 genes,8 taxa):Populus trichocarpaPOPTR_0001s22750.1
ORTHOMCL10040(8 genes,8 taxa):Sorghum bicolorSb07g005470.1
ORTHOMCL10040(8 genes,8 taxa):Carica papayaevm.TU.supercontig_50.124
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.oleraceaC08:31350109..33628428 (+)A.thalianaChr3:21609307..23437344 (+)253
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC08:27373536..34472409 (+)B.rapaA09:10065156..15472209 (+)727
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
NAT3G590402182134921824312Chr3Subgenome_III(LF)368
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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