PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Glyma.13G139000.1.p
Common NameGLYMA_13G139000, LOC100801182
Organism
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: 526aa    MW: 56452 Da    PI: 9.8021
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Glyma.13G139000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.13.2e-056587123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         + C++C+k F r  nL+ H r H
  Glyma.13G139000.1.p 65 FICEICNKGFQRDQNLQLHRRGH 87
                         89*******************88 PP

2zf-C2H213.90.00017141163123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC++C+k +  +s+ k H +t+
  Glyma.13G139000.1.p 141 WKCEKCSKKYAVQSDWKAHTKTC 163
                          58*******************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.4E-56487IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.02E-76487No hitNo description
PfamPF121716.3E-56587IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0226587IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8456587IPR007087Zinc finger, C2H2
PROSITE patternPS0002806787IPR007087Zinc finger, C2H2
SMARTSM00355110106136IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.6E-4129162IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.02E-7136161No hitNo description
SMARTSM00355130141161IPR015880Zinc 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: 526 aa     Download sequence    Send to blast
MQMMPGDPFS LSTSIGGFTQ DKQNTNPNPK PNPPPKKKRN LPGTPDPDAE VIALSPKTLM  60
ATNRFICEIC NKGFQRDQNL QLHRRGHNLP WKLRQRSNKE VRKKVYICPE QTCVHHDPAR  120
ALGDLTGIKK HFSRKHGEKK WKCEKCSKKY AVQSDWKAHT KTCGTREYKC DCGTLFSRKD  180
SFITHRAFCD ALAEESARLT SVTTTNLNFK SEEGGNNVMN SQQHGLGGHG LIGAQSLQNV  240
SGIPQFGSHG FRLDFNGMEQ QIRPSLSLWL NQGNHQMNSN NNNINSNNNS ASDAGPNYMS  300
SSGLPEIVQM AHANALMGCS SSMVSNFGGV HAGSNSSSAN LSLGKRGEAC GSTVVDLASI  360
YNNSEGQNKN SKPASPMSAT ALLQKAAQMG STRSTNPSIF SGSFGVINSP SSQTTSLNNN  420
NNGGAAMMLA SNTSTAAANA NDFSSLRHSS NSFDQLVMQT NAQLQSEPVK LKLHSNGMEN  480
NLTRDFLGVS GGGGGGGGPQ FLPQELGKFA SMGSPMGLSQ FTSNQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-37137206372Zinc finger protein JACKDAW
5b3h_F1e-37137206372Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
191103KLRQRSNKEVRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Gma.190360.0root| somatic embryo| vegetative bud
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.13G139000.1.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
GenBankAP0150410.0AP015041.1 Vigna angularis var. angularis DNA, chromosome 8, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003541407.10.0zinc finger protein JACKDAW
SwissprotQ700D21e-121IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLK7LZN20.0K7LZN2_SOYBN; Uncharacterized protein
STRINGGLYMA13G20231.10.0(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-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-AvendaƱo 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]