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 RrC1030_p3
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 HB-PHD
Protein Properties Length: 628aa    MW: 70159.4 Da    PI: 4.3722
Description HB-PHD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1030_p3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox283.8e-09548590853
                 -HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHH CS
    Homeobox   8 tkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRa 53 
                 t+  +++L + Fe+nryp+ ++re LAk+l++t   V+ WF N R 
  RrC1030_p3 548 TNPRTQRLFKSFEENRYPDITTRENLAKELEMT---VSSWFNNTRF 590
                 6667899***********************997...889****996 PP
2PHD39.99.9e-14200255151
                 SBTTTSSTCT..TSSEEEBSS.SSSEEETTTSTSSSSHHSHHSS..TBSSHHHHTT CS
         PHD   1 rCkvCgksde..egelvlCdg.CkewfHlkClglkleseekpeg..ewlCeeCkek 51 
                 +C+ Cg+++   +++++lCdg C++ fH++C++++l++e++p +  +wlC+ C++k
  RrC1030_p3 200 FCAKCGSKELpiDNDIILCDGfCDRGFHQYCVEPPLRKEDIPPDdeSWLCPGCNCK 255
                 6999**944356********88*******************99999*******975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579035.09E-14189255IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.104.2E-13196254IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS5001611.11198255IPR019787Zinc finger, PHD-finger
CDDcd155045.14E-26200252No hitNo description
PfamPF006283.9E-11200255IPR019787Zinc finger, PHD-finger
SMARTSM002493.1E-9200253IPR001965Zinc finger, PHD-type
PROSITE patternPS013590201252IPR019786Zinc finger, PHD-type, conserved site
SMARTSM003890.0012547599IPR001356Homeobox domain
PROSITE profilePS500718.989548595IPR001356Homeobox domain
PfamPF000461.1E-6548590IPR001356Homeobox domain
SuperFamilySSF466891.07E-8548595IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.601.6E-8551598IPR009057Homeodomain-like
CDDcd000867.26E-8552589No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 628 aa     Download sequence    Send to blast
MHSANRRRTR SSGSGLDQTN PEVDKVPPVV QSNASVPLQT PEAETLTKHV EEPTRNEGKG  60
ISNMVSSEEH KSTTPVTGKK SSGSHRELVL GLPCRGQFEI HRSSKKLGGG GVVSSHKRAK  120
RCEEAAGSSS VDVNAAPTPV DGSKKRKESV MRKSEVREDD EYTRIKKKLR YFLNRIRYEQ  180
SLIDAYSLEG WKEISSEDIF CAKCGSKELP IDNDIILCDG FCDRGFHQYC VEPPLRKEDI  240
PPDDESWLCP GCNCKDYSLD LLNESLGTKL SVSDSWEKVF PEAAAAMAGG GQSLDCDLPS  300
DDFEDEEYDP DGLNDKADDE DGSDDSDESE NEDGSCDESD CTSASDEMVE TFKEAKDIMD  360
LPSDDSEDDD YDPDAPVPDE DKMQECSDSD NTSDSEDLEA SFKGDESNQQ DEGKPGRKKS  420
QLPDVPISES DTGIDDDGLV DVPGRRKVER LDYKKLYDDE YENVPTSSSD DEDWDKTAGK  480
EDFESAEEGD NVPLKQHTEA EEHTSTKKPR QISKRESKKD TLKAPQEVPR ENGCSGGKSS  540
SAVYNKQTNP RTQRLFKSFE ENRYPDITTR ENLAKELEMT VSSWFNNTRF STNKRMASKE  600
DVEKLRTEVK GRHLLLEVAN KQWKLTQS
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1163169RIKKKLR
2443450GRRKVERL
Functional Description ? help Back to Top
Source Description
UniProtBinds only to large DNA fragments. Recognizes a DNA fragment carrying 8 copies of box7 motif of the light-induced cab-E promoter of Nicotiana plumbaginifolia. Also recognizes the box7m1 motif.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0256241e-31AB025624.1 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone: MLD14.
GenBankAK1171051e-31AK117105.1 Arabidopsis thaliana At3g19510 mRNA for putative homeobox protein HAT3.1, complete cds, clone: RAFL16-64-G01.
GenBankBT0059651e-31BT005965.1 Arabidopsis thaliana At3g19510 gene, complete cds.
GenBankCP0026861e-31CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
GenBankX695121e-31X69512.1 A.thaliana HAT3.1 mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018433119.10.0PREDICTED: homeobox protein HAT3.1-like
SwissprotQ049960.0HAT31_ARATH; Homeobox protein HAT3.1
TrEMBLA0A3P5ZFP40.0A0A3P5ZFP4_BRACM; Uncharacterized protein
STRINGBra038213.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM72702543
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G19510.10.0Homeodomain-like protein with RING/FYVE/PHD-type zinc finger domain
Publications ? help Back to Top
  1. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]