PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC1688_p5
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C2H2
Protein Properties Length: 388aa    MW: 44537.9 Da    PI: 7.0605
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1688_p5genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2110.00133355123
                EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                y C++Cg s s k++ ++Hi +H
  RrC1688_p5 33 YLCQYCGISRSKKYLITSHIESH 55
                56*******************96 PP
2zf-C2H220.21.6e-0681103123
                 EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                 ++C+ Cg  F+ + +Lk+H+++H
  RrC1688_p5  81 HTCQECGAEFKKPAHLKQHMQSH 103
                 79*******************99 PP
3zf-C2H217.21.4e-05109133123
                 EEET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                 + C   dC+ s++rk++L+rH+ tH
  RrC1688_p5 109 FACYvdDCTASYRRKDHLNRHLLTH 133
                 678888*****************99 PP
4zf-C2H2201.9e-06191214223
                 EET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2   2 kCp..dCgksFsrksnLkrHirtH 23 
                 +C+   Cgk F+ +s+L++H  +H
  RrC1688_p5 191 VCKevGCGKAFKYPSQLQKHEDSH 214
                 79999***************9888 PP
5zf-C2H220.31.5e-06281306123
                 EEET..TTTEEESSHHHHHHHHHH.T CS
     zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                 +kC+   C+ +Fs +snL++H++  H
  RrC1688_p5 281 FKCEveGCSSTFSKPSNLQKHLKAvH 306
                 89********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355263355IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.5E-879102IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015714.00481108IPR007087Zinc finger, C2H2
SMARTSM003550.001581103IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028083103IPR007087Zinc finger, C2H2
SuperFamilySSF576677.94E-1194135No hitNo description
Gene3DG3DSA:3.30.160.606.4E-13103135IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.66109138IPR007087Zinc finger, C2H2
SMARTSM003550.14109133IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280111133IPR007087Zinc finger, C2H2
PROSITE profilePS501579.556138168IPR007087Zinc finger, C2H2
SMARTSM003551.2138163IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280140163IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.0E-6183214IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.45190219IPR007087Zinc finger, C2H2
SMARTSM003550.0055190214IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280192214IPR007087Zinc finger, C2H2
SMARTSM003552.2222247IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280224247IPR007087Zinc finger, C2H2
SMARTSM0035525250271IPR015880Zinc finger, C2H2-like
SuperFamilySSF576671.75E-8261316No hitNo description
PROSITE profilePS5015712.84281311IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.2E-8281306IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003553.6E-4281306IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280283306IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.5E-5307333IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003554.9312338IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280314338IPR007087Zinc 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: 388 aa     Download sequence    Send to blast
MNPSPCVDTQ REMSEEEANL DVNPTKTKDI RNYLCQYCGI SRSKKYLITS HIESHHKMEV  60
EEERNEEACE DEEEEISGKQ HTCQECGAEF KKPAHLKQHM QSHSLERPFA CYVDDCTASY  120
RRKDHLNRHL LTHKGKLFKC PVENCKSEFS IHGNISKHVK KFHTDTYSNK DESVGGDSQP  180
SESSSDQKKL VCKEVGCGKA FKYPSQLQKH EDSHEKLDSV EAFCSEIGCM KYFTNEECLK  240
AHIRSCHQHV NCEICGSKHL KKNIKRHLRT HDEDSSSPGE FKCEVEGCSS TFSKPSNLQK  300
HLKAVHEDIR PFVCGFPGCG MRFAYKHVRN NHENSGSHIY TCGDFVEADE DFTSRPRGGL  360
KRKQVTAEML VRKRVMPPQF DSEEHETC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5wjq_D7e-16333419284Zinc finger protein 568
Search in ModeBase
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ6304780.0AJ630478.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At1g72050D.
GenBankAY0542250.0AY054225.1 Arabidopsis thaliana At1g72050/F28P5_6 mRNA, complete cds.
GenBankAY0660420.0AY066042.1 Arabidopsis thaliana At1g72050/F28P5_6 mRNA, complete cds.
GenBankAY1866100.0AY186610.1 Arabidopsis thaliana transcription factor IIIA (TFIIIA) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018446244.10.0PREDICTED: transcription factor IIIA-like
SwissprotQ84MZ40.0TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A3P6BJ380.0A0A3P6BJ38_BRACM; Uncharacterized protein (Fragment)
STRINGBo6g092790.10.0(Brassica oleracea)
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
AT1G72050.20.0transcription factor IIIA