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 Glyma.19G180400.1.p
Common NameGLYMA_19G180400, LOC100789331
Organism
Glycine max
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja
Family C2H2
Protein Properties Length: 511aa    MW: 55322.7 Da    PI: 9.4477
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Glyma.19G180400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.13.1e-056789123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         + C++C+k F r  nL+ H r H
  Glyma.19G180400.1.p 67 FICEICNKGFQRDQNLQLHRRGH 89
                         89*******************88 PP
2zf-C2H213.90.00016143165123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC++C+k +  +s+ k H +t+
  Glyma.19G180400.1.p 143 WKCEKCSKKYAVQSDWKAHTKTC 165
                          58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.02E-76689No hitNo description
Gene3DG3DSA:3.30.160.601.4E-56689IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.8456789IPR007087Zinc finger, C2H2
SMARTSM003550.0226789IPR015880Zinc finger, C2H2-like
PfamPF121716.1E-56789IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SMARTSM0035598108138IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.5E-5131164IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.02E-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: 511 aa     Download sequence    Send to blast
MQMIPGDPFS LSTSLPGLPN NEQNTNTNPN PNTPPPNKKK RNLPGTPDPD AEVIALSPKT  60
LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN KDIRKKVYIC PEKTCVHHDA  120
ARALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA HTKTCGTREY KCDCGTLFSR  180
KDSFITHRAF CDALAEESSR LTSVASTSLN FMSEDTTMMN TQASLSSSGL INGQGMQSVS  240
HFGPHGLRLM SMGTDQQRPN LSLWLNQGNH HINNPLDVAS SSSSGLPEVL HMAQPNNNAL  300
IGSSTMFSNF GITPASSNSS NPNLSLMGKK GEGGASDLAS MYSESQNKNS NSATPMSATA  360
LLQKAAQMGS TRSTNPSIFS GSFGVMSSSS TQSTSLNSNS NQSSDQLNHA FQNFNATSSS  420
ATLLGSSTNF SSLTHSSNGF DQFLMENNVE PTQLKLHPGS NIMEQHNLTR DFLGVSGNGG  480
GHHAFLPQEL AKFASLGSSM GLNQFTAGHQ *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-38139205369Zinc finger protein JACKDAW
5b3h_F5e-38139205369Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
193105KLRQRSNKDIRKK
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269|PubMed:17785527}.
UniprotTISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269|PubMed:17785527}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGlyma.19G180400.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by SCR and SHR. {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
GenBankAP0150371e-157AP015037.1 Vigna angularis var. angularis DNA, chromosome 4, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003553547.20.0zinc finger protein JACKDAW isoform X1
RefseqXP_028217223.10.0zinc finger protein JACKDAW-like isoform X1
SwissprotQ700D21e-136IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A445FI540.0A0A445FI54_GLYSO; Zinc finger protein JACKDAW
TrEMBLK7MZ050.0K7MZ05_SOYBN; Uncharacterized protein
STRINGGLYMA19G36430.20.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF18134275
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-101C2H2-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]