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 Carubv10005083m
Common NameCARUB_v10005083mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family bHLH
Protein Properties Length: 370aa    MW: 39974.2 Da    PI: 6.9969
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10005083mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH50.83e-16196242455
                      HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
              HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                       hn  E+rRR+riN+++  L++l+P++      K +Ka++L +A+eY+k+Lq
  Carubv10005083m 196 VHNLSEKRRRSRINEKMKALQSLIPNS-----NKTDKASMLDEAIEYLKQLQ 242
                      6*************************7.....5******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000831.03E-17188246No hitNo description
SuperFamilySSF474594.84E-20190252IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.063192241IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.101.6E-19193252IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.0E-13196242IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.0E-18198247IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007623Biological Processcircadian rhythm
GO:0009409Biological Processresponse to cold
GO:0010114Biological Processresponse to red light
GO:0010154Biological Processfruit development
GO:0010187Biological Processnegative regulation of seed germination
GO:0048440Biological Processcarpel development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 370 aa     Download sequence    Send to blast
MISQREEREE KKKKRVMGDK KLISSSSSLY DTRSSNHHPP SSSDEISLFL RHIFDRSSPL  60
PSYYSPATTT SMIGVHGDPH ADNSRCFLSQ HPPSDSAFMT TKRVGDFSEV LVGGSSAVGS  120
ASAAACFGFS GGGNNNAQGN SSGTRVSSSS VGASGNETDE YDCESEEGGE AVVDEAPSSK  180
SGPSRTSSKR CRAAEVHNLS EKRRRSRINE KMKALQSLIP NSNKTDKASM LDEAIEYLKQ  240
LQLQVQMLTM RNGVNLHPLC LPGTTLHPLQ LSQIRPPEAT NDPLLNHTNQ FTSNSNAPEM  300
INTVPSSYAL EPSIRSHFGP FPLLTSPVDM SREGGLAHQR LNLGHSNTNL TGEQAGFDGQ  360
QPDLKDRLT*
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269|PubMed:10225997, ECO:0000269|Ref.8}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00035PBMTransfer from AT4G36930Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10005083m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269|PubMed:11245574}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3195400.0AF319540.1 Arabidopsis thaliana SPATULA (SPT) mRNA, complete cds.
GenBankAK2292670.0AK229267.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor (AtbHLH024) / SPATULA (SPT), complete cds, clone: RAFL16-54-P05.
GenBankBT0264620.0BT026462.1 Arabidopsis thaliana At4g36930 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006283961.10.0transcription factor SPATULA
SwissprotQ9FUA40.0SPT_ARATH; Transcription factor SPATULA
TrEMBLR0GJ300.0R0GJ30_9BRAS; Uncharacterized protein
STRINGXP_006283961.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM41992754
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36930.11e-168bHLH family protein
Publications ? help Back to Top
  1. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  2. Pabón-Mora N,Wong GK,Ambrose BA
    Evolution of fruit development genes in flowering plants.
    Front Plant Sci, 2014. 5: p. 300
    [PMID:25018763]
  3. Moubayidin L,Ostergaard L
    Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development.
    Curr. Biol., 2014. 24(22): p. 2743-8
    [PMID:25455035]
  4. Pfannebecker KC,Lange M,Rupp O,Becker A
    Seed Plant-Specific Gene Lineages Involved in Carpel Development.
    Mol. Biol. Evol., 2017. 34(4): p. 925-942
    [PMID:28087776]
  5. Zumajo-Cardona C,Ambrose BA,Pabón-Mora N
    Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae).
    Evodevo, 2017. 8: p. 5
    [PMID:28331573]
  6. Reyes-Olalde JI, et al.
    The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium.
    PLoS Genet., 2017. 13(4): p. e1006726
    [PMID:28388635]
  7. Wu M, et al.
    SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis.
    Biochem. Biophys. Res. Commun., 2018. 503(4): p. 2380-2385
    [PMID:29966653]