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 Glyma.12G048600.1.p
Common NameGLYMA_12G048600, LOC100813285
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja
Family B3
Protein Properties Length: 442aa    MW: 50118.1 Da    PI: 9.4879
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Glyma.12G048600.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B359.46.3e-19696197
                         EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
                   B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92
                         f k l+ps v  +++l+lp +f++++gg+      +tl  ++g +W+v l  +k +++y++ +GWkeFvk   +  g  +vFk++g+s+f  
  Glyma.12G048600.1.p  6 FHKLLLPSTVQPNQQLRLPDNFMRKYGGE--LLPIVTLSVPDGSVWRVGL--KKADNKYWFLDGWKEFVKHYSISIGYLLVFKYEGKSSF-- 91
                         899***********************877..44599**************..*********************************99999.. PP

                         EEEEE CS
                   B3 93 vvkvf 97
                          v++f
  Glyma.12G048600.1.p 92 SVHIF 96
                         88887 PP

2B356.55.1e-18305395498
                          E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
                   B3   4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                          vl ps+  + ++++lp  fae+h +g++     ++l+ ++gr+W v++ yr+++    l++GW eF  +n+L egD++vF+l + +e  l
  Glyma.12G048600.1.p 305 VLRPSYLYRGCIMYLPSCFAEKHlNGVSG---FIKLQISNGRQWPVRCLYRGGR--AKLSQGWFEFSLENNLGEGDVCVFELLRMKEVVL 389
                          78899******************877743...59**************665555..66***********************998889989 PP

                          EEEEE- CS
                   B3  93 vvkvfr 98 
                           v+vfr
  Glyma.12G048600.1.p 390 QVTVFR 395
                          999998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.89E-23297IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.5E-24397IPR015300DNA-binding pseudobarrel domain
CDDcd100175.15E-23497No hitNo description
PROSITE profilePS5086314.466699IPR003340B3 DNA binding domain
PfamPF023621.9E-16696IPR003340B3 DNA binding domain
SMARTSM010197.4E-19699IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.103.4E-24294395IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.16E-24295395IPR015300DNA-binding pseudobarrel domain
CDDcd100171.52E-22300395No hitNo description
PROSITE profilePS5086313.479302397IPR003340B3 DNA binding domain
SMARTSM010194.6E-16302397IPR003340B3 DNA binding domain
PfamPF023629.5E-16305395IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 442 aa     Download sequence    Send to blast
MPHPSFHKLL LPSTVQPNQQ LRLPDNFMRK YGGELLPIVT LSVPDGSVWR VGLKKADNKY  60
WFLDGWKEFV KHYSISIGYL LVFKYEGKSS FSVHIFNLAT SEINYQSATR SSNEGLHFTN  120
RLKLFEEIED EDSIEISDSS PSHLAPSSLQ NQALTGSVDK MMPGKSYTPP ALQNLFNGSK  180
LNSINWGEGG NAHSSRIANS LDNRLTRDIG LQFNAVEFKR STEELKLRAS MEERMKKTTR  240
KKRKSVCASA DGQDPSAEHE EEVEMRLRFY ESASARKRTV TAEERERAIN AAKAFEPPNP  300
FCRVVLRPSY LYRGCIMYLP SCFAEKHLNG VSGFIKLQIS NGRQWPVRCL YRGGRAKLSQ  360
GWFEFSLENN LGEGDVCVFE LLRMKEVVLQ VTVFRVIEDV GLLSPPLQQN QNMSSAKMLN  420
TPLQQHLTST KMVRNQQQVH S*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-7226840015146B3 domain-containing transcription factor VRN1
4i1k_B1e-7226840015146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Gma.247850.0seed coat
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
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
PlantRegMapGlyma.12G048600.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU8574130.0EU857413.1 Glycine max reduced vernalization response 1 (VRN1) gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006592124.10.0B3 domain-containing transcription factor VRN1 isoform X1
SwissprotQ8L3W11e-131VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLI1LQ960.0I1LQ96_SOYBN; Uncharacterized protein
STRINGGLYMA12G05250.10.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF21473485
Representative plantOGRP20511436
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G49480.12e-74related to vernalization1 1
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]