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 Cagra.4084s0003.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family B3
Protein Properties Length: 228aa    MW: 26000.4 Da    PI: 10.0161
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.4084s0003.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.15.8e-17130223199
                          EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                          f  vl ps+  + ++++lp  fae++ +g++ +   ++  ++  ++W v++    k gr  +++GW eF  +n++ egD++vF+l ++++
  Cagra.4084s0003.1.p 130 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GF--IK-LQLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLRTRD 213
                          678899********************85452.33..44.44688*******..666666779************************99** PP

                          E..EEEEE-S CS
                   B3  90 felvvkvfrk 99 
                          f l+v++fr 
  Cagra.4084s0003.1.p 214 FILKVTAFRV 223
                          *9*9999985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.105.1E-23122222IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.32E-22123224IPR015300DNA-binding pseudobarrel domain
CDDcd100173.38E-21128222No hitNo description
PROSITE profilePS5086312.52130224IPR003340B3 DNA binding domain
SMARTSM010191.6E-19130224IPR003340B3 DNA binding domain
PfamPF023622.0E-15130223IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009409Biological Processresponse to cold
GO:0034613Biological Processcellular protein localization
GO:0005634Cellular Componentnucleus
GO:0005886Cellular Componentplasma membrane
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 228 aa     Download sequence    Send to blast
MDMNAAQNHF NKRARLFEDP NNRDARVMYP SNPTSAEQMN RGYGGSAAIQ SFFKDSKPEE  60
TPPKVLKKRG RKKKNPNPED INSSTPGGDD SENRSKFYES ASARKRTVTA EERERAVNAA  120
KTFEPANPFF RVVLRPSYLY RGCIMYLPSG FAEKYLSGIS GFIKLQLGEK QWPVRCLYKA  180
GRAKFSQGWY EFTLENNIGE GDVCVFELLR TRDFILKVTA FRVNEYM*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A2e-919622715146B3 domain-containing transcription factor VRN1
4i1k_B2e-919622715146B3 domain-containing transcription factor VRN1
Search in ModeBase
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00192DAPTransfer from AT1G49480Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.4084s0003.1.p
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
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
RefseqXP_006305572.11e-169B3 domain-containing protein REM19
RefseqXP_023645099.11e-169B3 domain-containing protein REM19
RefseqXP_023645100.11e-169B3 domain-containing protein REM19
RefseqXP_023645101.11e-169B3 domain-containing protein REM19
RefseqXP_023645102.11e-169B3 domain-containing protein REM19
RefseqXP_023645103.11e-169B3 domain-containing protein REM19
RefseqXP_023645104.11e-169B3 domain-containing protein REM19
SwissprotQ9XIB51e-151REM19_ARATH; B3 domain-containing protein REM19
TrEMBLR0IJ371e-168R0IJ37_9BRAS; Uncharacterized protein
STRINGCagra.4084s0003.1.p1e-169(Capsella grandiflora)
STRINGXP_006305572.11e-169(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM112428103
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G49480.11e-139related to vernalization1 1
Publications ? help Back to Top
  1. 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]
  2. 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]