PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Vradi09g09810.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
Family YABBY
Protein Properties Length: 224aa    MW: 24277 Da    PI: 9.5016
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Vradi09g09810.1genomeSNUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY22.82.8e-075917942156
            YABBY  42 Ctsllsvnlakas...qllaaeshldeslkeelleelkveeenlksnvekeesastsvssekl...senedeevprvppvirPPekrqrvPsay 129
                      C+ ++++n++ +    ++  ++s ++ ++++++++ +++   ++++   k    ++  + +     ++ +  ++++ +++ + P+k +r Psa+
  Vradi09g09810.1  59 CAVVMALNVSCNGgvfHADMVMSYFSGTGTQTMKNAKGKGAVKVSKEALKPVDDRKVGKRKAPskpDKGSAPKAKKEKKAKKDPNKPKRPPSAF 152
                      444555555554433344444555555555555555444444444444443333333333333112444555556666799************* PP

            YABBY 130 nrfikeeiqrikasnPdishreafsaa 156
                        f+ e  q  ka+nP++    a   a
  Vradi09g09810.1 153 FVFLEEFRQTFKAENPNVKAVSAVGKA 179
                      *****************9877776655 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF470952.62E-16130189IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.105.7E-14144190IPR009071High mobility group box domain
SMARTSM003984.1E-13144211IPR009071High mobility group box domain
PROSITE profilePS5011813.202145199IPR009071High mobility group box domain
CDDcd013901.51E-14145199No hitNo description
PfamPF005053.1E-14145190IPR009071High mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 224 aa     Download sequence    Send to blast
MLDSLKSREL LLCALSPNLA LPHVEWCVES HGSSLDLTCW WLLLVAFLCG GGHCSQRFCA  60
VVMALNVSCN GGVFHADMVM SYFSGTGTQT MKNAKGKGAV KVSKEALKPV DDRKVGKRKA  120
PSKPDKGSAP KAKKEKKAKK DPNKPKRPPS AFFVFLEEFR QTFKAENPNV KAVSAVGKAG  180
GEKWKSLSSA MHSETDKSKS EVNDEDDEAS AELLELPSLS YRT*
Functional Description ? help Back to Top
Source Description
UniProtBinds preferentially double-stranded DNA. Modulates general plant growth and stress tolerance. Confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. {ECO:0000269|PubMed:17114349, ECO:0000269|PubMed:9461286}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapVradi09g09810.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by salt stress. {ECO:0000269|PubMed:17169924}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0892344e-91BT089234.1 Soybean clone JCVI-FLGm-1O6 unknown mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_014515007.14e-59high mobility group B protein 1
RefseqXP_014515009.14e-59high mobility group B protein 1
RefseqXP_014515010.14e-59high mobility group B protein 1
RefseqXP_014515011.14e-59high mobility group B protein 1
RefseqXP_017442644.14e-59PREDICTED: high mobility group B protein 1
RefseqXP_017442645.14e-59PREDICTED: high mobility group B protein 1
RefseqXP_017442646.14e-59PREDICTED: high mobility group B protein 1
RefseqXP_017442648.14e-59PREDICTED: high mobility group B protein 1
SwissprotO495952e-45HMGB1_ARATH; High mobility group B protein 1
TrEMBLA0A0L9VTF19e-58A0A0L9VTF1_PHAAN; Uncharacterized protein
TrEMBLA0A0S3SWR79e-58A0A0S3SWR7_PHAAN; Uncharacterized protein
TrEMBLA0A1S3VA359e-58A0A1S3VA35_VIGRR; high mobility group B protein 1
STRINGXP_007133904.12e-55(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF492922
Publications ? help Back to Top
  1. Comella P, et al.
    Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1 locus on chromosome III.
    Plant Mol. Biol., 1999. 41(5): p. 687-700
    [PMID:10645728]
  2. Stemmer C,Leeming DJ,Franssen L,Grimm R,Grasser KD
    Phosphorylation of maize and Arabidopsis HMGB proteins by protein kinase CK2alpha.
    Biochemistry, 2003. 42(12): p. 3503-8
    [PMID:12653554]
  3. Elo A,Lyznik A,Gonzalez DO,Kachman SD,Mackenzie SA
    Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome.
    Plant Cell, 2003. 15(7): p. 1619-31
    [PMID:12837951]
  4. Launholt D,Merkle T,Houben A,Schulz A,Grasser KD
    Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus.
    Plant Cell, 2006. 18(11): p. 2904-18
    [PMID:17114349]
  5. Kwak KJ,Kim JY,Kim YO,Kang H
    Characterization of transgenic Arabidopsis plants overexpressing high mobility group B proteins under high salinity, drought or cold stress.
    Plant Cell Physiol., 2007. 48(2): p. 221-31
    [PMID:17169924]
  6. Launholt D,Grønlund JT,Nielsen HK,Grasser KD
    Overlapping expression patterns among the genes encoding Arabidopsis chromosomal high mobility group (HMG) proteins.
    FEBS Lett., 2007. 581(6): p. 1114-8
    [PMID:17316617]
  7. Lildballe DL, et al.
    The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance, and transcriptome in Arabidopsis.
    J. Mol. Biol., 2008. 384(1): p. 9-21
    [PMID:18822296]
  8. Pedersen DS,Grasser KD
    The role of chromosomal HMGB proteins in plants.
    Biochim. Biophys. Acta, 2010 Jan-Feb. 1799(1-2): p. 171-4
    [PMID:20123078]
  9. Pedersen DS, et al.
    Nucleocytoplasmic distribution of the Arabidopsis chromatin-associated HMGB2/3 and HMGB4 proteins.
    Plant Physiol., 2010. 154(4): p. 1831-41
    [PMID:20940346]
  10. Schrumpfová PP,Fojtová M,Mokroš P,Grasser KD,Fajkus J
    Role of HMGB proteins in chromatin dynamics and telomere maintenance in Arabidopsis thaliana.
    Curr. Protein Pept. Sci., 2011. 12(2): p. 105-11
    [PMID:21348847]
  11. Merkle T,Grasser KD
    Unexpected mobility of plant chromatin-associated HMGB proteins.
    Plant Signal Behav, 2011. 6(6): p. 878-80
    [PMID:21543902]
  12. Li MW,Zhou L,Lam HM
    Paraformaldehyde Fixation May Lead to Misinterpretation of the Subcellular Localization of Plant High Mobility Group Box Proteins.
    PLoS ONE, 2015. 10(8): p. e0135033
    [PMID:26270959]
  13. Roy A, et al.
    Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana.
    Plant Mol. Biol., 2016. 92(3): p. 371-88
    [PMID:27503561]
  14. Stemmer C,Ritt C,Igloi GL,Grimm R,Grasser KD
    Variability in Arabidopsis thaliana chromosomal high-mobility-group-1-like proteins.
    Eur. J. Biochem., 1997. 250(3): p. 646-52
    [PMID:9461286]