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 Gorai.013G040000.1
Common NameB456_013G040000, LOC105782416
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family B3
Protein Properties Length: 352aa    MW: 40263.9 Da    PI: 9.6727
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.013G040000.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3505.5e-16595197
                        EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS
                  B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93
                        ff +l+ s +l+++ l++p +f++++  +   s+   l+ ++g +W+v +  +k ++++++++GW+eF +   +++g ++vF+++g+s f   
  Gorai.013G040000.1  5 FFHKLILSTTLQEKKLRIPDNFVKKFRDE--LSVAAALTVPDGHVWRVGI--KKVDNKVWFQEGWQEFLERYYIRVGYVLVFRYEGNSAF--S 91
                        788999999**************999755..999****************..**********************************9999..8 PP

                        EEEE CS
                  B3 94 vkvf 97
                        v++f
  Gorai.013G040000.1 92 VSIF 95
                        8887 PP
2B365.58e-21249339498
                         E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS
                  B3   4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 
                         vl ps+  + ++++lp  fae+h +g++ +   ++l+ ++gr+W+v++ y++++    +++GW eF  +n+L egD++vF+l +++ef l+
  Gorai.013G040000.1 249 VLRPSYLYRGCIMYLPSCFAEKHlSGVS-G--SIKLQLPDGRQWSVRCLYKGGK--AKFSQGWYEFTLENNLGEGDVCVFELLRSREFVLK 334
                         78899******************86663.3..59999***********555555..6699**********************999****** PP

                         EEEE- CS
                  B3  94 vkvfr 98 
                         v+vfr
  Gorai.013G040000.1 335 VTVFR 339
                         ***98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019369.81E-21396IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.2E-21396IPR015300DNA-binding pseudobarrel domain
CDDcd100171.48E-17596No hitNo description
PfamPF023627.4E-13595IPR003340B3 DNA binding domain
PROSITE profilePS5086313.521598IPR003340B3 DNA binding domain
SMARTSM010191.2E-12698IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.107.2E-25238339IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.63E-24239339IPR015300DNA-binding pseudobarrel domain
CDDcd100172.99E-23244339No hitNo description
PROSITE profilePS5086313.958246341IPR003340B3 DNA binding domain
SMARTSM010197.1E-23246341IPR003340B3 DNA binding domain
PfamPF023621.2E-18249339IPR003340B3 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: 352 aa     Download sequence    Send to blast
MPRPFFHKLI LSTTLQEKKL RIPDNFVKKF RDELSVAAAL TVPDGHVWRV GIKKVDNKVW  60
FQEGWQEFLE RYYIRVGYVL VFRYEGNSAF SVSIFNLYNS EINYQTNALV GTQYNHGKQY  120
PFEQLEDDEC ISPALQNLFG GSKLNNCINW GGDANLQTSK GVNNQPIRVK LHTSGSGAMK  180
PEPKKRGRKR KFDPNVQDSS AGREDDVDMR FRCYESASAR KRTVTAEERE RAINAAKAFE  240
PTNPFCRVVL RPSYLYRGCI MYLPSCFAEK HLSGVSGSIK LQLPDGRQWS VRCLYKGGKA  300
KFSQGWYEFT LENNLGEGDV CVFELLRSRE FVLKVTVFRV MESGGLMHRS Q*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A5e-7421434217144B3 domain-containing transcription factor VRN1
4i1k_B5e-7421434217144B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Gra.31490.0flower|seedling| flowering
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJX5879931e-58JX587993.1 Gossypium hirsutum clone NBRI_GE22287 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012462594.10.0PREDICTED: B3 domain-containing transcription factor VRN1-like isoform X1
RefseqXP_016745120.10.0PREDICTED: B3 domain-containing transcription factor VRN1-like isoform X1
SwissprotQ8L3W11e-156VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A0D2TUM10.0A0A0D2TUM1_GOSRA; Uncharacterized protein
TrEMBLA0A1U8P1X60.0A0A1U8P1X6_GOSHI; B3 domain-containing transcription factor VRN1-like isoform X1
STRINGGorai.013G040000.10.0(Gossypium raimondii)
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
AT3G18990.11e-154B3 family protein
Publications ? help Back to Top
  1. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  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]