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 Ciclev10012016m
Common NameCICLE_v10012016mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family C2H2
Protein Properties Length: 367aa    MW: 42541.4 Da    PI: 8.5853
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10012016mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.30.0012547123
                     EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                     y C +Cg + s ks+  +Hi tH
  Ciclev10012016m 25 YYCDYCGICRSKKSLILSHIATH 47
                     89********************6 PP
2zf-C2H221.37.1e-076889223
                     EETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  2 kCpdCgksFsrksnLkrHirtH 23
                     +C+ Cg sF+ + +Lk+H+ +H
  Ciclev10012016m 68 TCEECGASFKKPAYLKQHMLSH 89
                     7*******************99 PP
3zf-C2H217.61.1e-0595119123
                      EEET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                      ++C+  dC+ s++rk++L+rH+ +H
  Ciclev10012016m  95 FRCSvdDCHASYRRKDHLTRHLLRH 119
                      89*********************99 PP
4zf-C2H215.26.2e-05124149123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                      +kCp  +C++ F+ + n+krH +  H
  Ciclev10012016m 124 FKCPieNCNREFTIQGNMKRHVKElH 149
                      89********************9986 PP
5zf-C2H218.17.1e-06164188123
                      EEET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                      y C+   Cgk+F+  s L++H  +H
  Ciclev10012016m 164 YICQeiGCGKVFKYASKLRQHEDSH 188
                      89*******************9888 PP
6zf-C2H215.45.4e-05255279223
                      EET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                      kC+   C  sFs++snL++H +  H
  Ciclev10012016m 255 KCQfkGCLLSFSTNSNLRQHVKAvH 279
                      688889**************99877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS501578.9332552IPR007087Zinc finger, C2H2
SMARTSM00355212547IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.5286794IPR007087Zinc finger, C2H2
SMARTSM003550.00886789IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.7E-76888IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SuperFamilySSF576673.12E-1075127No hitNo description
Gene3DG3DSA:3.30.160.608.0E-1189121IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.006695119IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.82795124IPR007087Zinc finger, C2H2
PROSITE patternPS00028097119IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.5E-6122146IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.55E-6122150No hitNo description
PROSITE profilePS5015710.637124155IPR007087Zinc finger, C2H2
SMARTSM003550.0015124149IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280126150IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.609.1E-8156188IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.39E-5160188No hitNo description
SMARTSM003550.0033164188IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.24164193IPR007087Zinc finger, C2H2
PROSITE patternPS000280166188IPR007087Zinc finger, C2H2
SMARTSM003553.6196221IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280198221IPR007087Zinc finger, C2H2
SMARTSM0035520224245IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.4E-6235276IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.92E-8236292No hitNo description
PROSITE profilePS5015710.928254284IPR007087Zinc finger, C2H2
SMARTSM003550.011254279IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280256279IPR007087Zinc finger, C2H2
SMARTSM003558.6285310IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280287311IPR007087Zinc 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: 367 aa     Download sequence    Send to blast
MEEVSDMEEE KGLEERPKSR VVRRYYCDYC GICRSKKSLI LSHIATHHKE DEERVDGDGE  60
TKGVQCNTCE ECGASFKKPA YLKQHMLSHL LERPFRCSVD DCHASYRRKD HLTRHLLRHQ  120
GKLFKCPIEN CNREFTIQGN MKRHVKELHH EGTTSTDSGD QKQYICQEIG CGKVFKYASK  180
LRQHEDSHVN LDSVEAFCSA PGCMKYFTNK QCLEAHIRSC HQYIPCEICG SMQLKKNIKR  240
HVRTHEARDL SERIKCQFKG CLLSFSTNSN LRQHVKAVHY EIKPFACSFF GCGMRFAFKH  300
VRDNHEKSGH HVYSSGDFVE SDERFRSRER GGRKRKCPTV EMLIRKRVTL PSPTQTCNTK  360
IDDTPD*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A3e-167122719165PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D3e-167122719165PROTEIN (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
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006430925.10.0transcription factor IIIA isoform X1
SwissprotQ84MZ41e-140TF3A_ARATH; Transcription factor IIIA
TrEMBLV4SYP10.0V4SYP1_9ROSI; Uncharacterized protein
STRINGXP_006430925.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM47142852
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.21e-134transcription factor IIIA