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.013G039800.1
Common NameB456_013G039800, LOC105782417
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: 237aa    MW: 26905.8 Da    PI: 9.9768
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.013G039800.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B365.76.8e-21134224498
                         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+   s  ++l+ ++gr+W+v++  r k+g+  +++GW eF  +n+L egD++vF+l +++e  l+
  Gorai.013G039800.1 134 VLRPSYLYRGCIMYLPSCFAEKHlSGV---SDSIKLQLPDGRQWSVRC--RYKGGKAKFSRGWYEFTLENNLGEGDVCVFELLRSREIVLK 219
                         7889*******************8666...336***************..667777779**********************9998888899 PP

                         EEEE- CS
                  B3  94 vkvfr 98 
                         v+vfr
  Gorai.013G039800.1 220 VTVFR 224
                         99998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.108.3E-25123224IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019368.44E-24125224IPR015300DNA-binding pseudobarrel domain
CDDcd100178.95E-25129224No hitNo description
SMARTSM010197.0E-22131226IPR003340B3 DNA binding domain
PROSITE profilePS5086314.254131226IPR003340B3 DNA binding domain
PfamPF023621.2E-18134224IPR003340B3 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: 237 aa     Download sequence    Send to blast
MKEIPRSVKQ YPFEQLQDNE CISPALQNMF GGSKLSNCIN WGGDVNRQNP KAVNNQPIRG  60
SGAMKPEPKK RGRKRKFDPN VQDSSAGRED DADMRLRCYE SASARKRTVT AEERERAINA  120
AKAFEPINPF CRVVLRPSYL YRGCIMYLPS CFAEKHLSGV SDSIKLQLPD GRQWSVRCRY  180
KGGKAKFSRG WYEFTLENNL GEGDVCVFEL LRSREIVLKV TVFRVMESGG LMHRSQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-719722715144B3 domain-containing transcription factor VRN1
4i1k_B1e-719722715144B3 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
GenBankJX5879936e-90JX587993.1 Gossypium hirsutum clone NBRI_GE22287 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012462596.11e-177PREDICTED: B3 domain-containing protein REM19-like
RefseqXP_012462597.11e-177PREDICTED: B3 domain-containing protein REM19-like
RefseqXP_016674964.11e-177PREDICTED: B3 domain-containing protein REM19-like
RefseqXP_017619827.11e-177PREDICTED: B3 domain-containing protein REM19-like
SwissprotQ8L3W11e-79VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A0B0PYM71e-175A0A0B0PYM7_GOSAR; B3 domain-containing transcription factor VRN1-like protein
TrEMBLA0A0D2W2K41e-175A0A0D2W2K4_GOSRA; Uncharacterized protein
TrEMBLA0A1U8IGH71e-175A0A1U8IGH7_GOSHI; B3 domain-containing protein REM19-like
STRINGGorai.013G039800.11e-176(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
AT3G18990.18e-78B3 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]