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 Sobic.006G180900.5.p
Common NameSb06g025550, SORBIDRAFT_06g025550
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family C2H2
Protein Properties Length: 536aa    MW: 55470.7 Da    PI: 8.2047
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.006G180900.5.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.41.3e-052446123
                          EEETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                          ++C+ C+k F r  nL+ H r H
  Sobic.006G180900.5.p 24 FVCEVCNKGFQREQNLQLHRRGH 46
                          89*******************88 PP
2zf-C2H211.70.00077101123123
                           EEETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                           +kC +C+k++  +s+ k H + +
  Sobic.006G180900.5.p 101 WKCDKCSKRYAVQSDWKAHSKIC 123
                           58*****************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.607.3E-62346IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.68E-72346No hitNo description
SMARTSM003550.00412446IPR015880Zinc finger, C2H2-like
PfamPF121713.4E-52446IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015711.0942446IPR007087Zinc finger, C2H2
PROSITE patternPS0002802646IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.5E-489122IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.68E-796121No hitNo description
SMARTSM00355140101121IPR015880Zinc 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: 536 aa     Download sequence    Send to blast
MELADPDAEV IALSPKTLLA TNRFVCEVCN KGFQREQNLQ LHRRGHNLPW KLKQKNPLQA  60
QRRRVYLCPE PTCVHHDPAR ALGDLTGIKK HFCRKHGEKK WKCDKCSKRY AVQSDWKAHS  120
KICGTREYRC DCGTLFSRRD SFITHRAFCD ALAQESARLP PTSLSSLTSH LYGATNAGNM  180
ALSLSQVGSH LTSTLQDGHH HHPSPELLRL GAAAGGGGSS IAARLDHLLS PNGASAFRSP  240
QAPPSSASFF LNAGASVGQD FGDDAGNGPH SYLQANKPFH GLMQLPDLQG NGAGGPGASG  300
PSLFNLGFFA NNGNSSGSSH EHASQGLMNN DQFSGGAGGG GGGGGSEVSA AGIFGGNFVG  360
GGDQVPPPGL YSDQASMLPQ MSATALLQKA AQMGATSSTN GGAASMFRGF VGSSSPHVRP  420
ATPHMEQSDA NLNDLMNSLA GGGVGGGGMF GGGNGAVSAG MFDPRQLCNM AEHEVKFGQG  480
GGDMTRDFLG VGGGGIVRGI STPRGGGGDH QSSSDMSSLE AEMKSASSFN GGRMP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-3497163369Zinc finger protein JACKDAW
5b3h_F1e-3497163369Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1333345SGGAGGGGGGGGS
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.171580.0root
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305|PubMed:22898356}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). 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). {ECO:0000269|PubMed:22898356, ECO:0000269|PubMed:24821766}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.006G180900.5.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY7548660.0AY754866.1 Zea mays INDETERMINATE-related protein 9 mRNA, complete cds.
GenBankBT0641200.0BT064120.1 Zea mays full-length cDNA clone ZM_BFc0139A11 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002446943.10.0protein indeterminate-domain 5, chloroplastic
RefseqXP_021318855.10.0protein indeterminate-domain 5, chloroplastic
SwissprotQ9ZUL31e-113IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A1Z5REH80.0A0A1Z5REH8_SORBI; Uncharacterized protein
STRINGSb06g025550.10.0(Sorghum bicolor)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G02670.11e-100indeterminate(ID)-domain 12
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]