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_009119357.1
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 C2H2
Protein Properties Length: 482aa    MW: 53071.3 Da    PI: 8.2113
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009119357.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.74.3e-057090323
                    ETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                    C++Cgk F r  nL+ H r H
  XP_009119357.1 70 CEICGKGFQRDQNLQLHRRGH 90
                    *******************88 PP
2zf-C2H213.40.00022144166123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     +kC++C+k++  +s+ k H +t+
  XP_009119357.1 144 WKCEKCSKRYAVQSDWKAHSKTC 166
                     58*****************9998 PP
3zf-C2H211.40.001174192523
                     TTTEEESSHHHHHHHHHHT CS
         zf-C2H2   5 dCgksFsrksnLkrHirtH 23 
                     dCg++Fsr++++ +H   +
  XP_009119357.1 174 DCGTVFSRRDSFITHRAFC 192
                     8**************8765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.49E-66790No hitNo description
Gene3DG3DSA:3.30.160.604.2E-56790IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.4896890IPR007087Zinc finger, C2H2
SMARTSM003550.0766890IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002807090IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-4132165IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.49E-6139164No hitNo description
SMARTSM00355130144164IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 482 aa     Download sequence    Send to blast
MTAEDQTISS SGGYVQSSST TDHVDHHHEL ESFNPPPAKK KRNLPGNPDP EAEVIALSPT  60
TLMATNRFLC EICGKGFQRD QNLQLHRRGH NLPWKLKQRT TKEVRKRVYV CPEKSCVHHH  120
PTRALGDLTG IKKHFCRKHG EKKWKCEKCS KRYAVQSDWK AHSKTCGTRE YRCDCGTVFS  180
RRDSFITHRA FCDALAEETA RLNAASHLKS LTSNNLNYHY LMGTLIPSPA PPPPFPFGPP  240
QPLQPHHFPI TTNTFDHHHH DVMKPASSLS LWMGGNNNHH QVTVDEGISP QDDYNWVFGN  300
ANNRGELITT SDSLITHENI NIVSSKENAN AATSLSVPSV FSSVDHITQD ANAASSAVAN  360
MSATALLQKA AQMGVTSSTP TTITTNQSTF HQIVEEGGSD KFFALFGPNS VGLMSKNGLQ  420
HEIENPRNGV TVASGIDELQ NYPLKRRRVE SGDAGGGGGQ TRDFLGVGVQ TMCHSSSING  480
WI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-36140215372Zinc finger protein JACKDAW
5b3h_F7e-36140215372Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1444448KRRRV
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009119357.1
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
PlantRegMapRetrieve-
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_009119357.10.0PREDICTED: zinc finger protein MAGPIE-like
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLM4DFJ80.0M4DFJ8_BRARP; Uncharacterized protein
STRINGBra015271.1-P0.0(Brassica rapa)
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]