PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G18000.1
Common NameMCM23.7, VDD
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family B3
Protein Properties Length: 307aa    MW: 35727 Da    PI: 10.2448
Description VERDANDI
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G18000.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B368.78.2e-2220113198
                  EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTE.EEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgr.yvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 
                  ffk+l ++d++++ + ++p + +++++  k +s++++l+ ++grsW+vk+  +k+++  y+  +GW++Fv++ngL e++ ++F+++ +++f  +v++f
  AT5G18000.1  20 FFKILRREDHSTEMMRMIPHHLIRSISD-KSSSFKMVLRVPWGRSWQVKI--SKNPNFhYMEDRGWNQFVNDNGLGENEYLTFTHEANMCF--NVTIF 112
                  99************************64.5799*****************..9***9966677**********************999***..99998 PP

                  - CS
           B3  98 r 98 
                  +
  AT5G18000.1 113 E 113
                  7 PP
2B346.56.6e-152283051597
                  -EE--HHH.HTT---..--SEEEEEETTS.-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
           B3  15 rlvlpkkfaeehggkkeesktltledesg.rsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 
                   l +pkkf++ h+  ++e+++ ++  ++g +sW+v++    ++ +  +++GW++ +k+ gL +gD+++Fkl++   +e++vkv 
  AT5G18000.1 228 FLGIPKKFVDMHM--PTETTMFKIHYPRGkKSWDVTY--VVTDVQSRFSGGWSRLAKELGLLVGDVCTFKLIK--PTEMRVKVS 305
                  368******9998..4567799999999889******..555555569**********************997..666688775 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.8E-2214116IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.75E-2215119IPR015300DNA-binding pseudobarrel domain
CDDcd100176.72E-2018112No hitNo description
PfamPF023628.5E-2020114IPR003340B3 DNA binding domain
PROSITE profilePS5086313.70420115IPR003340B3 DNA binding domain
SMARTSM010199.1E-2620115IPR003340B3 DNA binding domain
PROSITE profilePS5086311.406214307IPR003340B3 DNA binding domain
SuperFamilySSF1019366.87E-19214304IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.8E-17214306IPR015300DNA-binding pseudobarrel domain
CDDcd100173.04E-14215306No hitNo description
SMARTSM010191.9E-16217307IPR003340B3 DNA binding domain
PfamPF023625.6E-11228304IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009553Biological Processembryo sac development
GO:0009567Biological Processdouble fertilization forming a zygote and endosperm
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000018anatomyovule primordium
PO:0000229anatomyflower meristem
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009052anatomyflower pedicel
PO:0020021anatomyintegument
PO:0025022anatomycollective leaf structure
PO:0025074anatomyembryo sac
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001170developmental stageseed development stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 307 aa     Download sequence    Send to blast
MVKNKAFFGQ IMEERDNPAF FKILRREDHS TEMMRMIPHH LIRSISDKSS SFKMVLRVPW  60
GRSWQVKISK NPNFHYMEDR GWNQFVNDNG LGENEYLTFT HEANMCFNVT IFEADGTEML  120
RPRKTITSSS GRNKREERKS IYKDVKKEEE IESWSESSHP CHKTAESTSG RLTQKQELNL  180
RKKEADKTEK SKTSKKKKVE TVSNDSEAGT SSLIPEFKLT IKKSHLLFLG IPKKFVDMHM  240
PTETTMFKIH YPRGKKSWDV TYVVTDVQSR FSGGWSRLAK ELGLLVGDVC TFKLIKPTEM  300
RVKVSKE
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1180197RKKEADKTEKSKTSKKKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.712300.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible250071_at0.0
Expression AtlasAT5G18000-
AtGenExpressAT5G18000-
ATTED-IIAT5G18000-
Functional Description ? help Back to Top
Source Description
TAIREncodes VERDANDI (VDD), a putative transcription factor belonging to the reproductive meristem (REM) family. VDD is a direct target of the MADS domain ovule identity complex. Mutation in VDD affects embryo sac differentiation.
Function -- GeneRIF ? help Back to Top
  1. STK, SHP1, and SHP2 redundantly regulate VERDANDI. The vdd mutant shows defects during the fertilization process resulting in semisterility.
    [PMID: 20581305]
  2. Data indicate that SEEDSTICK (STK) and SEPALLATA3 (SEP3) dimers can induce loop formation in the VERDANDI (VDD) promoter by binding to two nearby CC(A/T)6GG (CArG) boxes essential for promoter activity.
    [PMID: 23847151]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G18000.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G18000
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2270350.0AK227035.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL09-55-P16.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_197301.10.0VERDANDI
SwissprotQ9FJG20.0Y5800_ARATH; B3 domain-containing protein At5g18000
TrEMBLA0A1P8BA450.0A0A1P8BA45_ARATH; VERDANDI
STRINGAT5G18000.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM56521135
Publications ? help Back to Top
  1. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  2. Matias-Hernandez L, et al.
    VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis.
    Plant Cell, 2010. 22(6): p. 1702-15
    [PMID:20581305]
  3. Mendes MA, et al.
    MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis.
    Plant Cell, 2013. 25(7): p. 2560-72
    [PMID:23847151]
  4. Mantegazza O, et al.
    Analysis of the arabidopsis REM gene family predicts functions during flower development.
    Ann. Bot., 2014. 114(7): p. 1507-15
    [PMID:25002525]
  5. Mendes MA, et al.
    Live and let die: a REM complex promotes fertilization through synergid cell death in Arabidopsis.
    Development, 2016. 143(15): p. 2780-90
    [PMID:27338615]