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.009G241600.1.p
Common NameSb09g029330, SORBIDRAFT_09g029330
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 C3H
Protein Properties Length: 332aa    MW: 35829.5 Da    PI: 7.739
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.009G241600.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH47.43e-15258282226
                           -S---SGGGGTS--TTTTT-SS-SS CS
               zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                           ktelC+ + +tG C+yGd+C+FaHg
  Sobic.009G241600.1.p 258 KTELCNKWEETGACPYGDQCQFAHG 282
                           9***********************8 PP
2zf-CCCH17.48.2e-06295320126
                           --S---SGGGGTS.--TTTTT-SS-SS CS
               zf-CCCH   1 yktelCrffartG.tCkyGdrCkFaHg 26 
                           ykt  Cr  ++ G  C+yG rC+F H+
  Sobic.009G241600.1.p 295 YKTQVCRMVLA-GvVCPYGHRCHFRHS 320
                           89999999999.66**********998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1000.103.3E-18252289IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.31E-10253288IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.244256284IPR000571Zinc finger, CCCH-type
SMARTSM003561.1E-8256283IPR000571Zinc finger, CCCH-type
PfamPF006422.6E-12258282IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.103.7E-11290320IPR000571Zinc finger, CCCH-type
SuperFamilySSF902298.5E-8291321IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.896294322IPR000571Zinc finger, CCCH-type
SMARTSM003563.7E-4294321IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051511Biological Processnegative regulation of unidimensional cell growth
GO:0061158Biological Process3'-UTR-mediated mRNA destabilization
GO:1901347Biological Processnegative regulation of secondary cell wall biogenesis
GO:0005829Cellular Componentcytosol
GO:0003730Molecular FunctionmRNA 3'-UTR binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 332 aa     Download sequence    Send to blast
MEVVAPAQHD ALHAAFGPKP FGGIGGDGRF SSSLSSLGGD RFFGYSTTTA SSCFGNSPGL  60
SSPSPRAASL SRGSSESGSV VDDGDDAADA ATVAERRLRL ARLALQYQEV VNRFELCLSY  120
LADASNEAAA LRRENDELRV ANEDLARRIE VVGCKLVDEF SSLRLAEEHA TPPPPPPPPP  180
SPLPVAPVMP KSISIRSPGY LKMNQNGKHR ASKPTKVSQR VFVGMDGGVK GEEERKGVEE  240
KKLNGGLEFE VYNQGMLKTE LCNKWEETGA CPYGDQCQFA HGIGELRPVI RHPRYKTQVC  300
RMVLAGVVCP YGHRCHFRHS VTPADLFLPR P*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1rgo_A2e-21258320567Butyrate response factor 2
Search in ModeBase
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.009G241600.1.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
GenBankEU9592350.0EU959235.1 Zea mays clone 212775 nucleic acid binding f mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002440301.10.0zinc finger CCCH domain-containing protein 39 isoform X1
SwissprotQ6L5G11e-105C3H39_ORYSJ; Zinc finger CCCH domain-containing protein 39
TrEMBLC5YW310.0C5YW31_SORBI; Uncharacterized protein
STRINGSb09g029330.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP27753784
Representative plantOGRP20581636
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G66810.12e-52C3H family protein
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]