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 29851.m002498
Common NameRCOM_0939270
Organism
Ricinus communis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family B3
Protein Properties Length: 333aa    MW: 38713.2 Da    PI: 9.6434
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
29851.m002498genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B345.21.7e-14696298
                   EEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS
             B3  2 fkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98
                   f +l+ s++ k + l++p +f++++g++   s   +l  + g +W v l   k ++++++++GW+eF +   +++g f+vF+++g+s f  +v++f+
  29851.m002498  6 FHKLILSNSIKDKKLRIPDNFVKKFGND--LSAFGRLSVPGGPVWPVGL--IKADDKFWFREGWQEFMERYSIRVGYFLVFRYEGHSVF--TVHIFN 96
                   56677899999999***********877..777899*************..9********************************99999..888885 PP
2B359.84.9e-19224314498
                    E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS
             B3   4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 
                    vl ps+  + ++++lp  fae+h +g++     ++l++++g++W v++ yr+++    l++GW eF  +n++ egD++vF+l ++++  l+v+vfr
  29851.m002498 224 VLRPSYLYRGCIMYLPSCFAEKHlNGVSG---FIKLQSSDGKQWPVRCLYRGGR--AKLSQGWYEFTLENNMGEGDVCVFELLKSRDIVLKVTVFR 314
                    78899******************877744...5***************665555..66***********************999889889999997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.04E-21397IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.0E-21398IPR015300DNA-binding pseudobarrel domain
CDDcd100177.86E-17496No hitNo description
PROSITE profilePS5086312.633598IPR003340B3 DNA binding domain
SMARTSM010192.1E-12698IPR003340B3 DNA binding domain
PfamPF023621.1E-11796IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.102.0E-24213314IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.49E-24214314IPR015300DNA-binding pseudobarrel domain
CDDcd100171.56E-21219314No hitNo description
SMARTSM010193.7E-19221316IPR003340B3 DNA binding domain
PROSITE profilePS5086313.676221316IPR003340B3 DNA binding domain
PfamPF023623.6E-17224314IPR003340B3 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: 333 aa     Download sequence    Send to blast
MPRPYFHKLI LSNSIKDKKL RIPDNFVKKF GNDLSAFGRL SVPGGPVWPV GLIKADDKFW  60
FREGWQEFME RYSIRVGYFL VFRYEGHSVF TVHIFNLSAS EINYQSNNTA GRRYLLFEDM  120
EDDDFVEHLS SSSPCLVPNS LKSDVRYYTP DAEAQKPKKR GRKKLKVDPN QQQPSAQQED  180
EVDMRFRFYE SASARKRTVT AEERERAINT AKTFEPMNPF CRVVLRPSYL YRGCIMYLPS  240
CFAEKHLNGV SGFIKLQSSD GKQWPVRCLY RGGRAKLSQG WYEFTLENNM GEGDVCVFEL  300
LKSRDIVLKV TVFRVLEGAG RMTQTLTTKY EQR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A8e-7518731715144B3 domain-containing transcription factor VRN1
4i1k_B8e-7518731715144B3 domain-containing transcription factor VRN1
Search in ModeBase
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap29851.m002498
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_015574592.10.0B3 domain-containing transcription factor VRN1 isoform X2
SwissprotQ8L3W11e-142VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLB9RZH60.0B9RZH6_RICCO; DNA binding protein, putative
STRINGXP_002519145.10.0(Ricinus communis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF21473485
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18990.11e-138B3 family protein
Publications ? help Back to Top
  1. 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]
  2. 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]