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.009G024400.1.p
Common NameSb09g002060, SORBIDRAFT_09g002060
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: 375aa    MW: 42288.1 Da    PI: 8.7459
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.009G024400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H222.13.8e-077697223
                          EETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2  2 kCpdCgksFsrksnLkrHirtH 23
                          +C+ Cg+sF+ + +Lk+H+++H
  Sobic.009G024400.1.p 76 ECQQCGMSFKKPAHLKQHMQSH 97
                          5*******************99 PP
2zf-C2H2193.8e-06103127123
                           EEET..TTTEEESSHHHHHHHHHHT CS
               zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                           ++C+   C+ s+srk++L+rH+ tH
  Sobic.009G024400.1.p 103 FSCTvdGCPLSYSRKDHLNRHLLTH 127
                           899999*****************99 PP
3zf-C2H215.84e-05132157123
                           EEET..TTTEEESSHHHHHHHHHH.T CS
               zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                           ++Cp   Cg+ F+ k n++rH +  H
  Sobic.009G024400.1.p 132 FVCPieGCGRKFNIKGNMQRHVQEiH 157
                           89*******************99877 PP
4zf-C2H222.92.2e-07169193123
                           EEET..TTTEEESSHHHHHHHHHHT CS
               zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                           ++Cp  +Cgk+F+  s+Lk+H  +H
  Sobic.009G024400.1.p 169 FVCPevNCGKTFKYASQLKKHEESH 193
                           89*******************9988 PP
5zf-C2H214.97.7e-05260284223
                           EET..TTTEEESSHHHHHHHHHH.T CS
               zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                           kC+  dC+ sFs ksnL +H +  H
  Sobic.009G024400.1.p 260 KCHfeDCKCSFSKKSNLDKHVKAvH 284
                           7*******************99877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355142850IPR015880Zinc finger, C2H2-like
SMARTSM003550.00567597IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.83875102IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.2E-57693IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS0002807797IPR007087Zinc finger, C2H2
SuperFamilySSF576671.54E-1187129No hitNo description
Gene3DG3DSA:3.30.160.601.2E-1494129IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.536103132IPR007087Zinc finger, C2H2
SMARTSM003550.0022103127IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280105127IPR007087Zinc finger, C2H2
SuperFamilySSF576672.06E-7113163No hitNo description
Gene3DG3DSA:3.30.160.603.6E-7130158IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.468132162IPR007087Zinc finger, C2H2
SMARTSM003551.4E-4132157IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280134157IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.3E-7165193IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.39E-5166195No hitNo description
PROSITE profilePS5015711.78169198IPR007087Zinc finger, C2H2
SMARTSM003550.0011169193IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280171193IPR007087Zinc finger, C2H2
SMARTSM0035512201226IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280203226IPR007087Zinc finger, C2H2
SMARTSM0035518229250IPR015880Zinc finger, C2H2-like
SuperFamilySSF576673.21E-6240301No hitNo description
Gene3DG3DSA:3.30.160.602.5E-4240281IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.843259289IPR007087Zinc finger, C2H2
SMARTSM003550.13259284IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280261284IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.3E-6283312IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.286290321IPR007087Zinc finger, C2H2
SMARTSM003551.8290316IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280292316IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005730Cellular Componentnucleolus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008097Molecular Function5S rRNA binding
GO:0046872Molecular Functionmetal ion binding
GO:0080084Molecular Function5S rDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 375 aa     Download sequence    Send to blast
MGEGGESGGG GGGGATTAAP PLRDIRRYKC GFCDVVRSKK CLLRAHVLEH HKDEVDALGG  60
YWEGGDGGPR KELSRECQQC GMSFKKPAHL KQHMQSHSLE RPFSCTVDGC PLSYSRKDHL  120
NRHLLTHEGK LFVCPIEGCG RKFNIKGNMQ RHVQEIHKDG SPCESKKEFV CPEVNCGKTF  180
KYASQLKKHE ESHVNLEYTE VICCEPGCMK FFSNVECLKA HNQSCHQHVR CDICGTKQLK  240
KNFQRHHRMH EGSCVTERVK CHFEDCKCSF SKKSNLDKHV KAVHEQRRPF VCQFSGCGKR  300
FSYKHVRDNH EKSSAHVRTE GDFVEADEQR PRSVGGRKRK PVSVESLMRK RVAAPDDGPA  360
HADGTEYLRW LLSG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A1e-178022320157PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D1e-178022320157PROTEIN (TRANSCRIPTION FACTOR IIIA)
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Both isoforms 1 and 2 transcripts are expressed in seedlings and both TFIIIA and TFIIIA-C are present at similar ratios in 10-day-old seedlings (at protein level). In correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length isoform 1 protein TFIIIA with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. Isoforms 1 and 2 transcripts accumulate in various tissues of the reproductive phase, including flowers and siliques, but only isoform 2 is present in mature seeds. In flowers, both TFIIIA and TFIIIA-C are present at similar ratios (at protein level). Very low amounts of TFIIIA are found in extracts from fresh siliques compared to TFIIIA-C. The amount of full-length TFIIIA protein progressively increases from fresh siliques to seeds concomitant with lower proportions of the shorter TFIIIA-C protein (at protein level) thus leading to 5S rRNA accumulation in the seed. {ECO:0000269|PubMed:22353599}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, flowers, siliques and seeds. {ECO:0000269|PubMed:22353599}.
Functional Description ? help Back to Top
Source Description
UniProtEssential protein (PubMed:22353599). Isoform 1 is a transcription activator the binds both 5S rDNA and 5S rRNA and stimulates the transcription of 5S rRNA gene (PubMed:12711688, PubMed:22353599). Isoform 1 regulates 5S rRNA levels during development (PubMed:22353599). {ECO:0000269|PubMed:12711688, ECO:0000269|PubMed:22353599}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00229DAPTransfer from AT1G72050Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.009G024400.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0668270.0BT066827.1 Zea mays full-length cDNA clone ZM_BFb0075I12 mRNA, complete cds.
GenBankKJ7268540.0KJ726854.1 Zea mays clone pUT3394 C2H2 transcription factor (C2H26) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002439194.10.0transcription factor IIIA
SwissprotQ84MZ41e-115TF3A_ARATH; Transcription factor IIIA
TrEMBLB5LXD80.0B5LXD8_SORBI; Transcription factor IIIA
STRINGSb09g002060.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP23823882
Representative plantOGRP29811627
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.21e-116transcription factor IIIA
Publications ? help Back to Top
  1. Fu Y, et al.
    Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA.
    Genome Res., 2009. 19(5): p. 913-21
    [PMID:19211543]