PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G18990.1
Common NameK13E13.10, REM39, VRN1
Organism
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: 341aa    MW: 39274.7 Da    PI: 9.5175
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G18990.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.74.5e-18595197
                 EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
           B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97
                 ff +l+ s++ +++rl++p kf+++++ +   s+ + l+ ++g +W+v l  rk ++++++++GW+eFv+   ++ g  ++F+++g+s f   v +f
  AT3G18990.1  5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKADNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF--SVYIF 95
                 899999*****************999755..99*****************..**********************************9999..88777 PP

2B355.11.4e-17244337199
                  EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 
                  f  vl ps+  + ++++lp  fae++ +g++ + ++++   +  ++W v++    k gr  +++GW eF  +n+L egD++vF+l ++++f l+v++f
  AT3G18990.1 244 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKVQ---LAEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAF 335
                  677899********************84442.444555...567*******..666666779************************99*******999 PP

                  -S CS
           B3  98 rk 99 
                  r 
  AT3G18990.1 336 RV 337
                  85 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.6E-23397IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.1E-22397IPR015300DNA-binding pseudobarrel domain
CDDcd100174.61E-19596No hitNo description
PfamPF023623.0E-15596IPR003340B3 DNA binding domain
PROSITE profilePS5086314.663598IPR003340B3 DNA binding domain
SMARTSM010192.7E-17598IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.104.3E-23236337IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.32E-22237338IPR015300DNA-binding pseudobarrel domain
CDDcd100171.79E-20242336No hitNo description
PfamPF023625.2E-16244337IPR003340B3 DNA binding domain
PROSITE profilePS5086312.619244338IPR003340B3 DNA binding domain
SMARTSM010198.1E-22244338IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009909Biological Processregulation of flower development
GO:0010048Biological Processvernalization response
GO:0005654Cellular Componentnucleoplasm
GO:0003677Molecular FunctionDNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 341 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKADNKIW  60
FQDGWQEFVD RYSIRIGYLL IFRYEGNSAF SVYIFNLSHS EINYHSTGLM DSAHNHFKRA  120
RLFEDLEDED AEVIFPSSVY PSPLPESTVP ANKGYASSAI QTLFTGPVKA EEPTPTPKIP  180
KKRGRKKKNA DPEEINSSAP RDDDPENRSK FYESASARKR TVTAEERERA INAAKTFEPT  240
NPFFRVVLRP SYLYRGCIMY LPSGFAEKYL SGISGFIKVQ LAEKQWPVRC LYKAGRAKFS  300
QGWYEFTLEN NLGEGDVCVF ELLRTRDFVL KVTAFRVNEY V
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-9420734112146B3 domain-containing transcription factor VRN
4i1k_B1e-9420734112146B3 domain-containing transcription factor VRN
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.275240.0bud| flower| root| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible256944_at0.0
Expression AtlasAT3G18990-
AtGenExpressAT3G18990-
ATTED-IIAT3G18990-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots and at lower levels in aerial parts. {ECO:0000269|PubMed:12114624}.
Functional Description ? help Back to Top
Source Description
TAIRRequired for vernalization. Essential for the complete repression of FLC in vernalized plants. Required for the methylation of histone H3
UniProtInvolved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner. {ECO:0000269|PubMed:12114624}.
Function -- GeneRIF ? help Back to Top
  1. Preliminary X-ray diffraction data analysis revealed that the VRN1(208-341) crystal diffracted to 2.1 A.
    [PMID: 19255487]
  2. Although VRN1 is sequence-nonspecific in DNA binding, it has a defined DNA-binding surface.
    [PMID: 23255593]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G18990.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G65480(A), AT2G03220(A), AT4G16845(R), AT5G10140(R)
Interaction ? help Back to Top
Source Intact With
IntActSearch Q8L3W1
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G18990
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0247310.0BT024731.1 Arabidopsis thaliana At3g18990 mRNA, complete cds.
GenBankAK2303880.0AK230388.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL25-06-L05.
GenBankAF2890520.0AF289052.1 Arabidopsis thaliana reduced vernalization response 1 (VRN1) mRNA, VRN1-Ler allele, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_188529.20.0B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLD7L9670.0D7L967_ARALL; Putative uncharacterized protein
STRINGAT3G18990.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP20511436
MalvidsOGEM112428103
Publications ? help Back to Top
  1. Sheldon CC,Rouse DT,Finnegan EJ,Peacock WJ,Dennis ES
    The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC).
    Proc. Natl. Acad. Sci. U.S.A., 2000. 97(7): p. 3753-8
    [PMID:10716723]
  2. Levy YY,Mesnage S,Mylne JS,Gendall AR,Dean C
    Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control.
    Science, 2002. 297(5579): p. 243-6
    [PMID:12114624]
  3. Prasad K,Kushalappa K,Vijayraghavan U
    Mechanism underlying regulated expression of RFL, a conserved transcription factor, in the developing rice inflorescence.
    Mech. Dev., 2003. 120(4): p. 491-502
    [PMID:12676326]
  4. Yan L, et al.
    Positional cloning of the wheat vernalization gene VRN1.
    Proc. Natl. Acad. Sci. U.S.A., 2003. 100(10): p. 6263-8
    [PMID:12730378]
  5. Sung S,Amasino RM
    Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3.
    Nature, 2004. 427(6970): p. 159-64
    [PMID:14712276]
  6. Bastow R, et al.
    Vernalization requires epigenetic silencing of FLC by histone methylation.
    Nature, 2004. 427(6970): p. 164-7
    [PMID:14712277]
  7. Sung S,Amasino RM
    Vernalization and epigenetics: how plants remember winter.
    Curr. Opin. Plant Biol., 2004. 7(1): p. 4-10
    [PMID:14732435]
  8. Loukoianov A,Yan L,Blechl A,Sanchez A,Dubcovsky J
    Regulation of VRN-1 vernalization genes in normal and transgenic polyploid wheat.
    Plant Physiol., 2005. 138(4): p. 2364-73
    [PMID:16055679]
  9. Jean Finnegan E, et al.
    The downregulation of FLOWERING LOCUS C (FLC) expression in plants with low levels of DNA methylation and by vernalization occurs by distinct mechanisms.
    Plant J., 2005. 44(3): p. 420-32
    [PMID:16236152]
  10. Trevaskis B,Hemming MN,Peacock WJ,Dennis ES
    HvVRN2 responds to daylength, whereas HvVRN1 is regulated by vernalization and developmental status.
    Plant Physiol., 2006. 140(4): p. 1397-405
    [PMID:16500994]
  11. Sheldon CC,Finnegan EJ,Dennis ES,Peacock WJ
    Quantitative effects of vernalization on FLC and SOC1 expression.
    Plant J., 2006. 45(6): p. 871-83
    [PMID:16507079]
  12. Mylne JS, et al.
    LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC.
    Proc. Natl. Acad. Sci. U.S.A., 2006. 103(13): p. 5012-7
    [PMID:16549797]
  13. Greb T, et al.
    The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC.
    Curr. Biol., 2007. 17(1): p. 73-8
    [PMID:17174094]
  14. Finnegan EJ,Dennis ES
    Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells.
    Curr. Biol., 2007. 17(22): p. 1978-83
    [PMID:17980595]
  15. Hemming MN,Peacock WJ,Dennis ES,Trevaskis B
    Low-temperature and daylength cues are integrated to regulate FLOWERING LOCUS T in barley.
    Plant Physiol., 2008. 147(1): p. 355-66
    [PMID:18359843]
  16. Li C,Dubcovsky J
    Wheat FT protein regulates VRN1 transcription through interactions with FDL2.
    Plant J., 2008. 55(4): p. 543-54
    [PMID:18433437]
  17. Dortay H, et al.
    Toward an interaction map of the two-component signaling pathway of Arabidopsis thaliana.
    J. Proteome Res., 2008. 7(9): p. 3649-60
    [PMID:18642946]
  18. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  19. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  20. Shimada S, et al.
    A genetic network of flowering-time genes in wheat leaves, in which an APETALA1/FRUITFULL-like gene, VRN1, is upstream of FLOWERING LOCUS T.
    Plant J., 2009. 58(4): p. 668-81
    [PMID:19175767]
  21. King G,Hill JM,Martin JL,Mylne JS
    Expression, purification and preliminary X-ray diffraction studies of VERNALIZATION1(208-341) from Arabidopsis thaliana.
    Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 2009. 65(Pt 3): p. 291-4
    [PMID:19255487]
  22. Greenup A,Peacock WJ,Dennis ES,Trevaskis B
    The molecular biology of seasonal flowering-responses in Arabidopsis and the cereals.
    Ann. Bot., 2009. 103(8): p. 1165-72
    [PMID:19304997]
  23. Hemming MN,Peacock WJ,Dennis ES,Trevaskis B
    Integration of seasonal flowering time responses in temperate cereals.
    Plant Signal Behav, 2008. 3(8): p. 601-2
    [PMID:19704811]
  24. Amasino R
    Seasonal and developmental timing of flowering.
    Plant J., 2010. 61(6): p. 1001-13
    [PMID:20409274]
  25. Greenup AG, et al.
    ODDSOC2 is a MADS box floral repressor that is down-regulated by vernalization in temperate cereals.
    Plant Physiol., 2010. 153(3): p. 1062-73
    [PMID:20431086]
  26. 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]
  27. Elrouby N,Coupland G
    Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(40): p. 17415-20
    [PMID:20855607]
  28. Mylne JS,Mas C,Hill JM
    NMR assignment and secondary structure of the C-terminal DNA binding domain of Arabidopsis thaliana VERNALIZATION1.
    Biomol NMR Assign, 2012. 6(1): p. 5-8
    [PMID:21553305]
  29. Kinjo H,Shitsukawa N,Takumi S,Murai K
    Diversification of three APETALA1/FRUITFULL-like genes in wheat.
    Mol. Genet. Genomics, 2012. 287(4): p. 283-94
    [PMID:22314801]
  30. Liang S, et al.
    Transcriptional Regulations on the Low-Temperature-Induced Floral Transition in an Orchidaceae Species, Dendrobium nobile: An Expressed Sequence Tags Analysis.
    Comp. Funct. Genomics, 2012. 2012: p. 757801
    [PMID:22550428]
  31. Jung CH,Wong CE,Singh MB,Bhalla PL
    Comparative genomic analysis of soybean flowering genes.
    PLoS ONE, 2012. 7(6): p. e38250
    [PMID:22679494]
  32. King GJ, et al.
    The Arabidopsis B3 domain protein VERNALIZATION1 (VRN1) is involved in processes essential for development, with structural and mutational studies revealing its DNA-binding surface.
    J. Biol. Chem., 2013. 288(5): p. 3198-207
    [PMID:23255593]
  33. Chen A,Dubcovsky J
    Wheat TILLING mutants show that the vernalization gene VRN1 down-regulates the flowering repressor VRN2 in leaves but is not essential for flowering.
    PLoS Genet., 2012. 8(12): p. e1003134
    [PMID:23271982]
  34. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  35. Chandler J,Wilson A,Dean C
    Arabidopsis mutants showing an altered response to vernalization.
    Plant J., 1996. 10(4): p. 637-44
    [PMID:8998499]