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_009138059.1
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: 770aa    MW: 85217.4 Da    PI: 7.4778
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009138059.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.82e-18283382198
                     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_009138059.1 283 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLKIQDIKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRTE-PEGK 375
                     99**************************555566778***************9989999999***9.********************654.7777 PP

                     .EEEEE- CS
              B3  92 lvvkvfr 98 
                     lv++ ++
  XP_009138059.1 376 LVMGYRK 382
                     7777665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.108.4E-30278386IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.49E-20280383IPR015300DNA-binding pseudobarrel domain
CDDcd100171.61E-22281382No hitNo description
SMARTSM010194.9E-20283383IPR003340B3 DNA binding domain
PROSITE profilePS5086311.053283384IPR003340B3 DNA binding domain
PfamPF023621.3E-15283382IPR003340B3 DNA binding domain
PROSITE profilePS5105014.8512562IPR011124Zinc finger, CW-type
PfamPF074968.5E-13517559IPR011124Zinc 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: 770 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 DQELQQLSGQ YPHLSNSKII PLFEKVLSAS DAGRIGRLVL  300
PKACAEAYFP PISQPEGLPL KIQDIKGKEW VFQFRFWPNN NSRMYVLEGV TPCIQSMQLQ  360
AGDTVTFSRT EPEGKLVMGY RKATNSTASQ MFKGSSEPNL NMFSNNLSSG CGDINWSKLD  420
KPEDMSKDGL MLQPSLISAR KRVRNIGTKS KRLLIDSVDV LELRLTWEEA QELLRPPQSA  480
KPSICTVEDH DFEEYDEPPV FGKRTVFVSR QTGEQEQWVQ CDACAKWRRL PVDTLLPPKW  540
LCSDNLLDPG RSSCSAPDEL TPREQDTLLR LSKEFKRRRL ASSNQEEASA LDTLANAAIT  600
TTGEQGETEV AATTKHPRHR AGCSCIVCSQ PPSGKGKHKP SCTCTVCEAV KRRFKTLMMR  660
KRNRGEAGQA SQQAQSDQCR EETEAESIPA VELPAAGGNI DLNSDPASRV SMMSLLQAAT  720
FPLEVYLKQK GVPNTAADQQ SSDIVSTENG SSSAAQEHDR DTSGAPEPMN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A1e-662573902131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1575579KRRRL
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_009138059.1
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_009138058.10.0PREDICTED: B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_009138059.10.0PREDICTED: B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_013719635.10.0B3 domain-containing transcription repressor VAL2-like isoform X1
RefseqXP_013719637.10.0B3 domain-containing transcription repressor VAL2-like isoform X1
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLM4E5B40.0M4E5B4_BRARP; 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]