PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G49480.1
Common NameF13F21.8, REM19, RTV1
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: 226aa    MW: 25850.2 Da    PI: 9.5287
Description related to vernalization1 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G49480.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.35.1e-17129222199
                  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++ egD++vF+l ++++f l v++f
  AT1G49480.1 129 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GF--IK-LQLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLRTRDFVLEVTAF 220
                  678899********************85452.33..44.44688*******..666666779************************99***9*99999 PP

                  -S CS
           B3  98 rk 99 
                  r 
  AT1G49480.1 221 RV 222
                  85 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.9E-23121222IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.16E-22122223IPR015300DNA-binding pseudobarrel domain
CDDcd100173.30E-21127221No hitNo description
PROSITE profilePS5086312.605129223IPR003340B3 DNA binding domain
PfamPF023621.8E-15129222IPR003340B3 DNA binding domain
SMARTSM010199.7E-21129223IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009409Biological Processresponse to cold
GO:0034613Biological Processcellular protein localization
GO:0005634Cellular Componentnucleus
GO:0005886Cellular Componentplasma membrane
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
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: 226 aa     Download sequence    Send to blast
MQMDSAQNQF NKRARLFEDP ELKDAKVIYP SNPESTEPVN KGYGGSTAIQ SFFKESKAEE  60
TPKVLKKRGR KKKNPNPEEV NSSTPGGDDS ENRSKFYESA SARKRTVTAE ERERAVNAAK  120
TFEPTNPYFR VVLRPSYLYR GCIMYLPSGF AEKYLSGISG FIKLQLGEKQ WPVRCLYKAG  180
RAKFSQGWYE FTLENNIGEG DVCVFELLRT RDFVLEVTAF RVNEYV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-919522615146B3 domain-containing transcription factor VRN1
4i1k_B1e-919522615146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.244800.0bud| floral meristem| flower| leaf| root| silique| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO425626240.0
Genevisible262400_at0.0
Expression AtlasAT1G49480-
AtGenExpressAT1G49480-
ATTED-IIAT1G49480-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:22232549}.
Functional Description ? help Back to Top
Source Description
UniProtInvolved in the regulation of vernalization (By similarity). Binds to DNA in vitro in a non-sequence-specific manner. XLG2 promotes the DNA binding activity of RTV1 specifically to promoter regions of FT and SOC1 in vivo and thus leads to the activation of floral integrator genes. {ECO:0000250, ECO:0000269|PubMed:22232549}.
Function -- GeneRIF ? help Back to Top
  1. a Ca(2+)-dependent G protein, XLG2, promotes RTV1 DNA binding activity for a subset of floral integrator genes and contributes to floral transition.
    [PMID: 22232549]
  2. These findings suggest that RTV1 and ITN1 regulate the subcellular localization of each other.
    [PMID: 22664102]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00192DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G49480.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By cold. {ECO:0000269|PubMed:22232549}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9XIB5
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G49480
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0156820.0BT015682.1 Arabidopsis thaliana At1g49480 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001322051.11e-167related to vernalization1 1
RefseqNP_001322052.11e-167related to vernalization1 1
RefseqNP_564547.11e-167related to vernalization1 1
SwissprotQ9XIB51e-168REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A178WGV01e-165A0A178WGV0_ARATH; RTV1
STRINGAT1G49480.11e-166(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM112428103
Representative plantOGRP20511436
Publications ? help Back to Top
  1. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  2. 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]
  3. Conte MG,Gaillard S,Droc G,Perin C
    Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
    BMC Genomics, 2008. 9: p. 183
    [PMID:18426584]
  4. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  5. Heo JB,Sung S,Assmann SM
    Ca2+-dependent GTPase, extra-large G protein 2 (XLG2), promotes activation of DNA-binding protein related to vernalization 1 (RTV1), leading to activation of floral integrator genes and early flowering in Arabidopsis.
    J. Biol. Chem., 2012. 287(11): p. 8242-53
    [PMID:22232549]
  6. Sakamoto H, et al.
    Interaction between a plasma membrane-localized ankyrin-repeat protein ITN1 and a nuclear protein RTV1.
    Biochem. Biophys. Res. Commun., 2012. 423(2): p. 392-7
    [PMID:22664102]
  7. 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]