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 NNU_005667-RA
Organism
Nelumbo nucifera
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Proteales; Nelumbonaceae; Nelumbo
Family C2H2
Protein Properties Length: 545aa    MW: 58954.2 Da    PI: 9.4485
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
NNU_005667-RAgenomeCASView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.11.6e-056789123
                   EEETTTTEEESSHHHHHHHHHHT CS
        zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                   ++C++C+k F r  nL+ H r H
  NNU_005667-RA 67 FVCEICNKGFQRDQNLQLHRRGH 89
                   89*******************88 PP
2zf-C2H213.80.00017143165123
                    EEETTTTEEESSHHHHHHHHHHT CS
        zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                    +kC++C+k +  +s+ k H +t+
  NNU_005667-RA 143 WKCEKCSKKYAVQSDWKAHTKTC 165
                    58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.8E-56689IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.94E-76689No hitNo description
SMARTSM003550.0176789IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.9496789IPR007087Zinc finger, C2H2
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SMARTSM00355110108138IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.6E-4131164IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.94E-7138163No hitNo description
SMARTSM00355130143163IPR015880Zinc 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: 545 aa     Download sequence    Send to blast
MQMMSGDGLS IPSSVRGFPQ EPISNPNPNP PNANPVVKKK RNLPGTPDPD AEVIALSPKT  60
LMATNRFVCE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRTS KEIRKRVYIC PEKSCVHHDP  120
SRALGDLTGI KKHFSRKHGE KKWKCEKCSK KYAVQSDWKA HTKTCGTREY KCDCGTLFSR  180
KDSFITHRAF CDALAEESAR LTSAAATNLN FRTDSINDAT STMPHGFGGR GGPNATAGIP  240
PLCPVFRPEF AGPEATNVLD ANRQKPRLSL WLDQANSHLN PIDAAANSNA FLATSSTGLP  300
ELVQMASTNM FSSSSSLVDY GGCVQPQWPS TGGNLSLSTS PRGLKEENGN KGQLVESLAP  360
LYSNNNQNQQ ANSAHMSATA LLQKAAQMGS TRSNPSLLGS FGVVSSSSSD TTSFNPHVQN  420
RNEFHQLMRQ AANQPENINE LMNSISTATA TTGVGDGMVG GLNLSSLTGT VNNLDRLMIP  480
QGGKQGQSVP VPQKFLSTAN EVEHSLTRDF LGVGGDAGRP FLQQELAKFA SMGSAMNLSQ  540
YSSTH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-38139208372Zinc finger protein JACKDAW
5b3h_F5e-38139208372Zinc finger protein JACKDAW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:20356954, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:28211915}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010253625.10.0PREDICTED: zinc finger protein JACKDAW-like
RefseqXP_019052874.10.0PREDICTED: zinc finger protein JACKDAW-like
SwissprotQ700D21e-123IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A1U8Q2320.0A0A1U8Q232_NELNU; zinc finger protein JACKDAW-like
STRINGXP_010253625.10.0(Nelumbo nucifera)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-104C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  2. Hirano Y, et al.
    Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
    Nat Plants, 2017. 3: p. 17010
    [PMID:28211915]
  3. Kobayashi A,Miura S,Kozaki A
    INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves.
    Plant Mol. Biol., 2017. 94(1-2): p. 1-13
    [PMID:28324206]
  4. Long Y, et al.
    In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
    Nature, 2017. 548(7665): p. 97-102
    [PMID:28746306]
  5. Bustillo-Avendaño E, et al.
    Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.
    Plant Physiol., 2018. 176(2): p. 1709-1727
    [PMID:29233938]