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 Ciclev10012412m
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: 282aa    MW: 32733.4 Da    PI: 9.1838
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10012412mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.17.6e-061034123
                     EEET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCp..dCgksFsrksnLkrHirtH 23
                     ++C+  dC+ s++rk++L+rH+ +H
  Ciclev10012412m 10 FRCSvdDCHASYRRKDHLTRHLLRH 34
                     89*********************99 PP
2zf-C2H215.74.4e-053964123
                     EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2  1 ykCp..dCgksFsrksnLkrHirt.H 23
                     +kCp  +C++ F+ + n+krH +  H
  Ciclev10012412m 39 FKCPieNCNREFTIQGNMKRHVKElH 64
                     89********************9986 PP
3zf-C2H218.65.1e-0679103123
                      EEET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                      y C+   Cgk+F+  s L++H  +H
  Ciclev10012412m  79 YICQeiGCGKVFKYASKLRQHEDSH 103
                      89*******************9888 PP
4zf-C2H215.83.9e-05170194223
                      EET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                      kC+   C  sFs++snL++H +  H
  Ciclev10012412m 170 KCQfkGCLLSFSTNSNLRQHVKAvH 194
                      688889**************99877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.08E-7136No hitNo description
Gene3DG3DSA:3.30.160.602.0E-9736IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.8271039IPR007087Zinc finger, C2H2
SMARTSM003550.00661034IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002801234IPR007087Zinc finger, C2H2
SuperFamilySSF576672.0E-63765No hitNo description
Gene3DG3DSA:3.30.160.601.7E-63761IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00153964IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.6373970IPR007087Zinc finger, C2H2
PROSITE patternPS0002804165IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.3E-871103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.72E-575103No hitNo description
SMARTSM003550.003379103IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.2479108IPR007087Zinc finger, C2H2
PROSITE patternPS00028081103IPR007087Zinc finger, C2H2
SMARTSM003553.6111136IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280113136IPR007087Zinc finger, C2H2
SMARTSM0035520139160IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.2E-6150191IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576676.17E-8151207No hitNo description
SMARTSM003550.011169194IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.928169199IPR007087Zinc finger, C2H2
PROSITE patternPS000280171194IPR007087Zinc finger, C2H2
SMARTSM003558.6200225IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280202226IPR007087Zinc 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: 282 aa     Download sequence    Send to blast
MLSHLLERPF RCSVDDCHAS YRRKDHLTRH LLRHQGKLFK CPIENCNREF TIQGNMKRHV  60
KELHHEGTTS TDSGDQKQYI CQEIGCGKVF KYASKLRQHE DSHVNLDSVE AFCSAPGCMK  120
YFTNKQCLEA HIRSCHQYIP CEICGSMQLK KNIKRHVRTH EARDLSERIK CQFKGCLLSF  180
STNSNLRQHV KAVHYEIKPF ACSFFGCGMR FAFKHVRDNH EKSGHHVYSS GDFVESDERF  240
RSRERGGRKR KCPTVEMLIR KRVTLPSPTQ TCNTKIDDTP D*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A6e-12114234165PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D6e-12114234165PROTEIN (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
SwissprotQ84MZ43e-89TF3A_ARATH; Transcription factor IIIA
TrEMBLV4SYP10.0V4SYP1_9ROSI; Uncharacterized protein
TrEMBLV4UWQ40.0V4UWQ4_9ROSI; Uncharacterized protein
STRINGXP_006430925.10.0(Citrus clementina)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.17e-84transcription factor IIIA