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 Ciclev10029038m
Common NameCICLE_v10028642mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family B3
Protein Properties Length: 274aa    MW: 31162.6 Da    PI: 9.7784
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10029038mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B362.95.1e-20172263499
                      E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEE CS
               B3   4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkv 96 
                      vl ps+  k ++++lp  fae+h +g+  ++  ++l+ ++g++W v++ yr+++    +++GW eF  +n+L egD++vF++ + +ef l+v+v
  Ciclev10029038m 172 VLRPSYLYKGCIMYLPSCFAEKHlNGV--CG-FIKLQLSDGKQWPVRCLYRGGR--AKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTV 260
                      7889*******************8777..44.59999999********666665..5699*********************9988********* PP

                      E-S CS
               B3  97 frk 99 
                      fr 
  Ciclev10029038m 261 FRV 263
                      996 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-24161263IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.7E-24164265IPR015300DNA-binding pseudobarrel domain
CDDcd100171.00E-22167262No hitNo description
PROSITE profilePS5086313.126169264IPR003340B3 DNA binding domain
SMARTSM010193.4E-21169264IPR003340B3 DNA binding domain
PfamPF023627.0E-18172263IPR003340B3 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
Sequence ? help Back to Top
Protein Sequence    Length: 274 aa     Download sequence    Send to blast
MPRPYFHKLI LASTIRDKRL RIPENFVRNF KDDLSAAATL IVPNEMEDDD SEHVDQPTVN  60
KTFNPPSFQN LLNSSKLSNS INGAGEANLQ RLKVKLYSQD GETPKLKKPG RKRKIDPNVQ  120
ASSAQEVHDG EMQFRFYESA SARKRTVTAE ERERAINAAK AFEPSNPFCR VVLRPSYLYK  180
GCIMYLPSCF AEKHLNGVCG FIKLQLSDGK QWPVRCLYRG GRAKFSQGWY EFTVENRLGE  240
GDVCVFEVLR AREFVLKVTV FRVSESAGFM SRH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A3e-7613526515144B3 domain-containing transcription factor VRN1
4i1k_B3e-7613526515144B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots and at lower levels in aerial parts. {ECO:0000269|PubMed:12114624}.
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:22232549}.
Functional Description ? help Back to Top
Source Description
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}.
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}.
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006423106.10.0B3 domain-containing transcription factor VRN1 isoform X2
SwissprotQ8L3W16e-80VRN1_ARATH; B3 domain-containing transcription factor VRN1
SwissprotQ9XIB52e-80REM19_ARATH; B3 domain-containing protein REM19
TrEMBLV4SH510.0V4SH51_9ROSI; Uncharacterized protein
STRINGXP_006479395.11e-169(Citrus sinensis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G49480.12e-82related 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]
  3. Kumar A,Singh A,Panigrahy M,Sahoo PK,Panigrahi KCS
    Carbon nanoparticles influence photomorphogenesis and flowering time in Arabidopsis thaliana.
    Plant Cell Rep., 2018. 37(6): p. 901-912
    [PMID:29541883]