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 orange1.1g030283m
Common NameCISIN_1g030283mg
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family YABBY
Protein Properties Length: 181aa    MW: 20064 Da    PI: 4.9374
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g030283mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY22.92.6e-07209085157
              YABBY  85 nvekeesastsvsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaa 157
                        n+ k    +++ ++ kl++ ++++ +r +++ + P+k +r Psa+  f+ e  +  k +nP+++   a   aa
  orange1.1g030283m  20 NDRKV--GKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAA 90 
                        44433..3455566679999999999999********************999999********9999998877 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF470955.11E-2641125IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.104.3E-2553127IPR009071High mobility group box domain
SMARTSM003988.9E-2554125IPR009071High mobility group box domain
PfamPF005052.9E-2455124IPR009071High mobility group box domain
PROSITE profilePS5011819.55855124IPR009071High mobility group box domain
CDDcd000849.13E-1555120No hitNo description
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: 181 aa     Download sequence    Send to blast
MKGAKGKGAA RVSQEALKPN DRKVGKRKAA TAKLDSGSKR QGKREKKAKK DPNKPKRPPS  60
AFFVFLEEFR KTFKKENPNV TAVSAVGKAA GGKWKSMSPA EKAPYESKAE KLKSEYGKKM  120
NAYNKKQDGD EASDKSKSEV NDEDEASGEE EHQLEPEPEP EQDEDEEVEE DEDDEEDDDD  180
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1j3c_A1e-1549126379High mobility group protein 2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.100670.0callus
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in cotyledons, roots, stems, leaves and flowers (excluding pedicels). {ECO:0000269|PubMed:17169924, ECO:0000269|PubMed:17316617, ECO:0000269|PubMed:9461286}.
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}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by salt stress. {ECO:0000269|PubMed:17169924}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006429363.11e-98high mobility group B protein 1
RefseqXP_006429364.11e-98high mobility group B protein 1
RefseqXP_006481020.12e-98high mobility group B protein 1-like
RefseqXP_006481021.12e-98high mobility group B protein 1-like
SwissprotO495952e-58HMGB1_ARATH; High mobility group B protein 1
TrEMBLA0A067E9361e-121A0A067E936_CITSI; Uncharacterized protein
STRINGXP_006481020.16e-98(Citrus sinensis)
STRINGXP_006429363.15e-98(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM640622
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]