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 Sobic.006G180900.1.p
Common NameSb06g025550, SORBIDRAFT_06g025550
Organism
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: 600aa    MW: 61772.9 Da    PI: 8.6779
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.006G180900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.21.5e-0588110123
                           EEETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                           ++C+ C+k F r  nL+ H r H
  Sobic.006G180900.1.p  88 FVCEVCNKGFQREQNLQLHRRGH 110
                           89*******************88 PP

2zf-C2H211.60.00088165187123
                           EEETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                           +kC +C+k++  +s+ k H + +
  Sobic.006G180900.1.p 165 WKCDKCSKRYAVQSDWKAHSKIC 187
                           58*****************9876 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.21E-787110No hitNo description
Gene3DG3DSA:3.30.160.608.3E-687110IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.004188110IPR015880Zinc finger, C2H2-like
PfamPF121713.9E-588110IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015711.09488110IPR007087Zinc finger, C2H2
PROSITE patternPS00028090110IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.604.1E-4153186IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.21E-7160185No hitNo description
SMARTSM00355140165185IPR015880Zinc 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: 600 aa     Download sequence    Send to blast
MASNSSAAAF FGVRDGDQQD QIKPLISPQQ QLAAALPGVA GAVPAASGQG APTAAAPQPP  60
PKKKRTMPDP DAEVIALSPK TLLATNRFVC EVCNKGFQRE QNLQLHRRGH NLPWKLKQKN  120
PLQAQRRRVY LCPEPTCVHH DPARALGDLT GIKKHFCRKH GEKKWKCDKC SKRYAVQSDW  180
KAHSKICGTR EYRCDCGTLF SRRDSFITHR AFCDALAQES ARLPPTSLSS LTSHLYGATN  240
AGNMALSLSQ VGSHLTSTLQ DGHHHHPSPE LLRLGAAAGG GGSSIAARLD HLLSPNGASA  300
FRSPQAPPSS ASFFLNAGAS VGQDFGDDAG NGPHSYLQAN KPFHGLMQLP DLQGNGAGGP  360
GASGPSLFNL GFFANNGNSS GSSHEHASQG LMNNDQFSGG AGGGGGGGGS EVSAAGIFGG  420
NFVGGGDQVP PPGLYSDQAS MLPQMSATAL LQKAAQMGAT SSTNGGAASM FRGFVGSSSP  480
HVRPATPHME QSDANLNDLM NSLAGGGVGG GGMFGGGNGA VSAGMFDPRQ LCNMAEHEVK  540
FGQGGGDMTR DFLGVGGGGI VRGISTPRGG GGDHQSSSDM SSLEAEMKSA SSFNGGRMP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C9e-35161230370Zinc finger protein JACKDAW
5b3h_F9e-35161230370Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1397409SGGAGGGGGGGGS
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.006G180900.1.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-114IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLC5YE140.0C5YE14_SORBI; Uncharacterized protein
STRINGSb06g025550.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP17333798
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G50700.11e-102indeterminate(ID)-domain 2
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]