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 Carubv10008897m
Common NameCARUB_v10008897mg
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 C2H2
Protein Properties Length: 509aa    MW: 56203.5 Da    PI: 8.3372
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10008897mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.64.6e-057393323
                     ETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                     C++Cgk F r  nL+ H r H
  Carubv10008897m 73 CEICGKGFQRDQNLQLHRRGH 93
                     *******************88 PP
2zf-C2H210.90.0015147169123
                      EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                      +kC++C k++  +s+ k H +t+
  Carubv10008897m 147 WKCEKCAKRYAVQSDWKAHSKTC 169
                      58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.604.5E-57093IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.37E-67093No hitNo description
PROSITE profilePS5015711.4897193IPR007087Zinc finger, C2H2
PROSITE patternPS0002807393IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.6E-4135168IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.37E-6142167No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 509 aa     Download sequence    Send to blast
MTAEDQTISS SGGYVQSSST TDHVDHHHHH HEHESLNPPL AKKKRNLPGN PDPEAEVIAL  60
SPKTLMATNR FLCEICGKGF QRDQNLQLHR RGHNLPWKLK QRTSKEVRKR VYVCPEKSCV  120
HHHPTRALGD LTGIKKHFCR KHGEKKWKCE KCAKRYAVQS DWKAHSKTCG TREYRCDCGT  180
IFSRRDSFIT HRAFCDALAE ETARLNAASH LKSLAATAGS NLNYHYLMGT LIQSPSPQPP  240
PSFPFGPSST EHHHHHFPIT TFDHHQDAMK PTSSLSLWMG GNINHHQQVT IEDRITRQPQ  300
PHSPHEDYNW VFGNENNRGE LITTSDSLIT HENNINTVQS KENANAATSL SVPSLFSSVD  360
QITQDANAAV TANMSATALL QKAAQMGATS SSTPPTTTIT TDQSAFLQSF ASKVSDQSQI  420
IEDGGSDKFF ALFGSNSAGL MSNNGLHEFG NPRSGVTVVS GIDELQNYPW KRRRVETGDA  480
GGGGQTRDFL GVGVQQKICH SSSINGWI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-35143210370Zinc finger protein JACKDAW
5b3h_F3e-35143210370Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1470474KRRRV
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAPTransfer from AT1G03840Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10008897m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4934280.0AB493428.1 Arabidopsis thaliana At1g03840 mRNA for hypothetical protein, partial cds, clone: RAAt1g03840.
GenBankAK2278370.0AK227837.1 Arabidopsis thaliana mRNA for putative DNA-binding protein, complete cds, clone: RAFL14-40-M12.
GenBankBT0062090.0BT006209.1 Arabidopsis thaliana At1g03840 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006307283.10.0zinc finger protein MAGPIE
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLR0GWJ50.0R0GWJ5_9BRAS; Uncharacterized protein
STRINGXP_006307283.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM37102660
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.10.0C2H2 family protein
Publications ? help Back to Top
  1. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]