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 XP_009138060.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family B3
Protein Properties Length: 766aa    MW: 84715.9 Da    PI: 7.4781
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009138060.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.82e-18279378198
                     EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                     f+kvl+ sd+++ grlvlpk +ae++   ++++e+  l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+F++++  e++
  XP_009138060.1 279 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLKIQDIKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRTE-PEGK 371
                     99**************************555566778***************9989999999***9.********************654.7777 PP

                     .EEEEE- CS
              B3  92 lvvkvfr 98 
                     lv++ ++
  XP_009138060.1 372 LVMGYRK 378
                     7777665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.2E-30272382IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.49E-20276379IPR015300DNA-binding pseudobarrel domain
CDDcd100171.60E-22277378No hitNo description
PROSITE profilePS5086311.053279380IPR003340B3 DNA binding domain
SMARTSM010194.9E-20279379IPR003340B3 DNA binding domain
PfamPF023621.3E-15279378IPR003340B3 DNA binding domain
PROSITE profilePS5105014.8508558IPR011124Zinc finger, CW-type
PfamPF074968.4E-13513555IPR011124Zinc 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: 766 aa     Download sequence    Send to blast
MESTKVCMNA QCGSTSTSGE WKRGWPMRSG ELASLCDKCG SAYEQSIFCQ VFHAEESGWR  60
ECNSCDKRLH CGCIASRFMM EVVDNGGVTC ISCAKKSGLF SMNVESNGRE FPTFASAEHV  120
SSVLERTNLK HLLHFQRISP TQPFLQMKQE ESLLPARLEA LRHNTEKKES AQPNLSISLG  180
PTLMTSPFHD VDDRSKTTTP IFQLASRSRQ LLPKPANSAP TTAPPMEPNG SLVSQIHVAR  240
PPPEGRGKTQ LLPRYWPRIT DQELQQLSGH SNSKIIPLFE KVLSASDAGR IGRLVLPKAC  300
AEAYFPPISQ PEGLPLKIQD IKGKEWVFQF RFWPNNNSRM YVLEGVTPCI QSMQLQAGDT  360
VTFSRTEPEG KLVMGYRKAT NSTASQMFKG SSEPNLNMFS NNLSSGCGDI NWSKLDKPED  420
MSKDGLMLQP SLISARKRVR NIGTKSKRLL IDSVDVLELR LTWEEAQELL RPPQSAKPSI  480
CTVEDHDFEE YDEPPVFGKR TVFVSRQTGE QEQWVQCDAC AKWRRLPVDT LLPPKWLCSD  540
NLLDPGRSSC SAPDELTPRE QDTLLRLSKE FKRRRLASSN QEEASALDTL ANAAITTTGE  600
QGETEVAATT KHPRHRAGCS CIVCSQPPSG KGKHKPSCTC TVCEAVKRRF KTLMMRKRNR  660
GEAGQASQQA QSDQCREETE AESIPAVELP AAGGNIDLNS DPASRVSMMS LLQAATFPLE  720
VYLKQKGVPN TAADQQSSDI VSTENGSSSA AQEHDRDTSG APEPMN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A8e-692573862131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1571575KRRRL
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
PlantRegMapXP_009138060.1
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_009138060.10.0PREDICTED: B3 domain-containing transcription repressor VAL2 isoform X2
RefseqXP_013719638.10.0B3 domain-containing transcription repressor VAL2-like isoform X2
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLA0A397KY290.0A0A397KY29_BRACM; Uncharacterized protein
STRINGBra023968.1-P0.0(Brassica rapa)
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]