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 Glyma.12G048600.2.p
Common NameGLYMA_12G048600
Organism
Glycine max
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: 410aa    MW: 46549 Da    PI: 9.4822
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Glyma.12G048600.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B339.21.3e-1211693597
                         EEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
                   B3 35 tltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97
                          +tl  ++g +W+v l  +k +++y++ +GWkeFvk   +  g  +vFk++g+s+f   v++f
  Glyma.12G048600.2.p 11 IVTLSVPDGSVWRVGL--KKADNKYWFLDGWKEFVKHYSISIGYLLVFKYEGKSSF--SVHIF 69
                         588999**********..*********************************99999..88887 PP
2B356.74.5e-18273363498
                          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.12G048600.2.p 273 VLRPSYLYRGCIMYLPSCFAEKHlNGVSG---FIKLQISNGRQWPVRCLYRGGR--AKLSQGWFEFSLENNLGEGDVCVFELLRMKEVVL 357
                          78899******************877743...59**************665555..66***********************998899989 PP

                          EEEEE- CS
                   B3  93 vvkvfr 98 
                           v+vfr
  Glyma.12G048600.2.p 358 QVTVFR 363
                          999998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5086312.464172IPR003340B3 DNA binding domain
SMARTSM010190.0085172IPR003340B3 DNA binding domain
CDDcd100176.70E-15170No hitNo description
SuperFamilySSF1019361.45E-15270IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.4E-16270IPR015300DNA-binding pseudobarrel domain
PfamPF023625.9E-101169IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.102.9E-24262363IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.8E-24263363IPR015300DNA-binding pseudobarrel domain
CDDcd100171.55E-22268363No hitNo description
PROSITE profilePS5086313.479270365IPR003340B3 DNA binding domain
SMARTSM010194.6E-16270365IPR003340B3 DNA binding domain
PfamPF023628.3E-16273363IPR003340B3 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: 410 aa     Download sequence    Send to blast
MRKYGGELLP IVTLSVPDGS VWRVGLKKAD NKYWFLDGWK EFVKHYSISI GYLLVFKYEG  60
KSSFSVHIFN LATSEINYQS ATRSSNEGLH FTNRLKLFEE IEDEDSIEIS DSSPSHLAPS  120
SLQNQALTGS VDKMMPGKSY TPPALQNLFN GSKLNSINWG EGGNAHSSRI ANSLDNRLTR  180
DIGLQFNAVE FKRSTEELKL RASMEERMKK TTRKKRKSDG QDPSAEHEEE VEMRLRFYES  240
ASARKRTVTA EERERAINAA KAFEPPNPFC RVVLRPSYLY RGCIMYLPSC FAEKHLNGVS  300
GFIKLQISNG RQWPVRCLYR GGRAKLSQGW FEFSLENNLG EGDVCVFELL RMKEVVLQVT  360
VFRVIEDVGL LSPPLQQNQN MSSAKMLNTP LQQHLTSTKM VRNQQQVHS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A9e-7323636815146B3 domain-containing transcription factor VRN1
4i1k_B9e-7323636815146B3 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.12G048600.2.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_003541121.10.0B3 domain-containing transcription factor VRN1 isoform X2
SwissprotQ8L3W11e-121VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A0R0HBZ20.0A0A0R0HBZ2_SOYBN; Uncharacterized protein
STRINGGLYMA12G05250.10.0(Glycine max)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18990.18e-75B3 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]