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 Rsa1.0_00092.1_g00032.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family B3
Protein Properties Length: 797aa    MW: 88161.1 Da    PI: 7.5007
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00092.1_g00032.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.72.1e-18281380198
                              EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvF 82 
                              f+kvl+ sd+++ grlvlpk +ae++   ++++e+  l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+F
  Rsa1.0_00092.1_g00032.1 281 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLKIQDIKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTF 365
                              99**************************555566778***************9989999999***9.******************* PP

                              EE-SSSEE..EEEEE- CS
                       B3  83 kldgrsefelvvkvfr 98 
                              ++++  e++lv++ ++
  Rsa1.0_00092.1_g00032.1 366 SRTE-PEGKLVMGYRK 380
                              *654.77777777665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.104.9E-30273384IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.28E-20278381IPR015300DNA-binding pseudobarrel domain
CDDcd100171.74E-22279380No hitNo description
PfamPF023621.4E-15281380IPR003340B3 DNA binding domain
PROSITE profilePS5086311.053281382IPR003340B3 DNA binding domain
SMARTSM010194.9E-20281381IPR003340B3 DNA binding domain
PROSITE profilePS5105014.8538588IPR011124Zinc finger, CW-type
PfamPF074968.8E-13543585IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:2000034Biological Processregulation of seed maturation
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 797 aa     Download sequence    Send to blast
MESTKVCMNA QCGSTSTSGD WKRGWPMRSG ELASLCDKCG SAYEQSIFCQ VFHAEESGWR  60
ECSSCDKRLH CGCIASRFMM ELLDNGGVTC ISCAKKSGLF YMSICHETNG RDFPTFASAE  120
HVSSVLERTN LKHLLHFQRI SPTQPFLQMK QEESLLPARL DPLRHKKESQ ESSAHPNLSI  180
SLGPTLMTSL PFHDAAVVVD DRSKTTPVFH LASRSRQLLP KPANSAPAPV ESSIVSQIHV  240
ARPPPEGRGK TQLLPRYWPR ITDQELQQLS GHSNSKIVPL FEKVLSASDA GRIGRLVLPK  300
ACAEAYFPPI SQPEGLPLKI QDIKGKEWVF QFRFWPNNNS RMYVLEGVTP CIQSMQLQAG  360
DTVTFSRTEP EGKLVMGYRK ATNSTAAQMF KGSSEPNLNM FSNNLSSGCG DINWSKLDKS  420
EDMSKDSLLL QPSLISARKR VRNIGTKSKR LLIDSVDVLE LRLTWEEAQE LLRPPQSAKP  480
SICTVEDHDF EEYDVSCSLP VIFFPLKQLR PLHCIHVLDA TQEPPVFGKR TVFVSRQTGE  540
QEQWVQCDAC AKWRRLPVDT LLPPKWLCSD NLLDPGRSSC SAPDELTPRE QDTLLRLSKE  600
FKRRRLASSN QEEASALDTL ANAAITTTGE QGETEVAATT KHPRHRAGCS CIVCSQPPSG  660
KGKHKPSCTC TVCEAVKRRF KTLMMRKRNR EEAGQASQQA QSECREETEA ESIPAVELPA  720
AAAGGNIDLN SDPASRVSMM SLLQAATFPL EAYLKQKAVP NTAAEQQSSD IVSTENGSSS  780
AAQEHDRDTS GAPEPLN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A3e-692593882131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1601605KRRRL
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL1/HSI2. {ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00092.1_g00032.1
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_018465394.10.0PREDICTED: B3 domain-containing transcription repressor VAL2-like
RefseqXP_018465395.10.0PREDICTED: B3 domain-containing transcription repressor VAL2-like
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLA0A397KY290.0A0A397KY29_BRACM; Uncharacterized protein
STRINGBra023968.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM72032639
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G32010.10.0HSI2-like 1
Publications ? help Back to Top
  1. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  2. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  3. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  4. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]