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 Solyc10g077110.1.1
Organism
Solanum lycopersicum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family C2H2
Protein Properties Length: 373aa    MW: 42852.8 Da    PI: 7.8373
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc10g077110.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.42.5e-056585323
                        ETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                        C+ Cg +F  + +Lk+H+++H
  Solyc10g077110.1.1 65 CEECGATFQKPAHLKQHLQSH 85
                        *******************99 PP
2zf-C2H217.79.6e-0691115123
                         EEET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                         ++C+  dC  s++rk++L rH+ +H
  Solyc10g077110.1.1  91 FVCHidDCQSSYRRKDHLSRHLLLH 115
                         89********************998 PP
3zf-C2H214.10.00014120145123
                         EEET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                         ++Cp   C+ +Fs + n++rH +  H
  Solyc10g077110.1.1 120 FECPvdGCKSTFSFQGNMTRHVKEmH 145
                         89********************9988 PP
4zf-C2H219.92e-06159183123
                         EEET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                         y+C+   Cgk+F+  s L++H  +H
  Solyc10g077110.1.1 159 YVCSeaGCGKVFKYASKLRKHEDSH 183
                         99*******************9888 PP
5zf-C2H217.71e-05250274223
                         EET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                         kC+  dC  +Fs++snL +Hi+  H
  Solyc10g077110.1.1 250 KCEfqDCLHTFSSRSNLAQHIKAvH 274
                         79999****************9888 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355261941IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.45E-1061115No hitNo description
SMARTSM003550.0196385IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.3186390IPR007087Zinc finger, C2H2
PROSITE patternPS0002806585IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.2E-76590IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.68191120IPR007087Zinc finger, C2H2
SMARTSM003550.06391115IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.8E-1091117IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028093115IPR007087Zinc finger, C2H2
SuperFamilySSF576671.19E-5101145No hitNo description
Gene3DG3DSA:3.30.160.603.4E-5118146IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0031120145IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.286120150IPR007087Zinc finger, C2H2
PROSITE patternPS000280122145IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.8E-7156183IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576676.07E-5157183No hitNo description
PROSITE profilePS5015711.427159188IPR007087Zinc finger, C2H2
SMARTSM003550.001159183IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280161183IPR007087Zinc finger, C2H2
SMARTSM003556191216IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280193216IPR007087Zinc finger, C2H2
SMARTSM0035521219240IPR015880Zinc finger, C2H2-like
SuperFamilySSF576676.05E-9230287No hitNo description
SMARTSM003550.006249274IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.214249279IPR007087Zinc finger, C2H2
PROSITE patternPS000280251274IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.6E-5254278IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
Gene3DG3DSA:3.30.160.604.8E-5279302IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.6280306IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280282306IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 373 aa     Download sequence    Send to blast
MGEVGEEKRE VVFRDIRRYY CEFCGLCRSK KSLISSHIQS HHQDVIESLK DDATENAKGS  60
KMNICEECGA TFQKPAHLKQ HLQSHSLERP FVCHIDDCQS SYRRKDHLSR HLLLHQGKLF  120
ECPVDGCKST FSFQGNMTRH VKEMHDQPAS AEVDLPKEYV CSEAGCGKVF KYASKLRKHE  180
DSHVKLETVE AMCLEPGCMK HFTNEKCLKE HIESCHQHID CEICGTKQLK KNIKRHLRTH  240
EEGPISERIK CEFQDCLHTF SSRSNLAQHI KAVHVGSKPF SCSISGCGMK FAFKHVRDKH  300
EQSGCHVYTP GDFEEVDEQF LSRPRGGRKR EPTLFESIMR KRITPPSGID PVFNQTPEYL  360
SWLRSMESDN QM*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A4e-176721119155PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D4e-176721119155PROTEIN (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
PlantRegMapSolyc10g077110.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ8821790.0Lycopersicon esculentum transcription factor IIIA mRNA, complete cds
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001234471.10.0transcription factor IIIA
SwissprotQ84MZ41e-139TF3A_ARATH; Transcription factor IIIA
TrEMBLQ06HM70.0Q06HM7_SOLLC; Transcription factor IIIA
STRINGSolyc10g077110.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA36442447
Representative plantOGRP29811627
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.21e-131transcription factor IIIA
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. 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]