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 RrC4900_p1
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 HD-ZIP
Protein Properties Length: 720aa    MW: 78471.6 Da    PI: 5.2625
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC4900_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox38.22.4e-1260952156
                HSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
    Homeobox 21 knrypsaeereeLAkklgLterqVkvWFqNrRakek 56
                ++++p+ ++r+eL++ l L+  qVk+WFqN+R+++k
  RrC4900_p1 60 QCPHPDDKQRKELSRDLCLEPLQVKFWFQNKRTQMK 95
                699******************************998 PP
2START213.11e-662304491206
                 HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEEEECT CS
       START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetleviss 87 
                 ela +a++elv++a++++p+Wv+     e +n++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +     +a tlev+s+
  RrC4900_p1 230 ELAVAAMEELVRMAQSGDPLWVSTGnsmELLNEEEYFRTFPRGIGpkqlgLRTEASRESAVVIMNHINLVEILMDVN-QWSCVFSgivsRALTLEVLST 327
                 57899******************9998899************999********************************.********************* PP

                 T......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHH CS
       START  88 g......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvdlkgrlphw 179
                 g      galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds +++     + R +++pSg+li++++ng+skvtw+eh+++++r++h 
  RrC4900_p1 328 GvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPNL----ISRTRRRPSGCLIQELPNGYSKVTWIEHMEVDDRSVHT 422
                 *******************************************************96....7999********************************** PP

                 HHHHHHHHHHHHHHHHHHHHTXXXXXX CS
       START 180 llrslvksglaegaktwvatlqrqcek 206
                 ++++lv+sgla+gak+wv+tl+rqce+
  RrC4900_p1 423 MYKPLVHSGLAFGAKRWVSTLERQCER 449
                 *************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003898.5E-453101IPR001356Homeobox domain
CDDcd000861.45E-95998No hitNo description
SuperFamilySSF466893.63E-1060101IPR009057Homeodomain-like
PfamPF000466.7E-106095IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.602.0E-1260105IPR009057Homeodomain-like
PROSITE profilePS5007111.7746297IPR001356Homeobox domain
PROSITE patternPS0002707295IPR017970Homeobox, conserved site
PROSITE profilePS5084845.039221452IPR002913START domain
SuperFamilySSF559611.51E-35222451No hitNo description
CDDcd088753.04E-125225448No hitNo description
SMARTSM002349.7E-73230449IPR002913START domain
PfamPF018528.9E-56231449IPR002913START domain
Gene3DG3DSA:3.30.530.204.1E-5327448IPR023393START-like domain
SuperFamilySSF559611.24E-25469708No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009845Biological Processseed germination
GO:0009913Biological Processepidermal cell differentiation
GO:0048497Biological Processmaintenance of floral organ identity
GO:0048825Biological Processcotyledon development
GO:0005634Cellular Componentnucleus
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 720 aa     Download sequence    Send to blast
MFESHHMFDM TTKSTSDNDL GITGSREDEF ETKSGTEVTT ENPSGEELQD PNQRPNKKKQ  60
CPHPDDKQRK ELSRDLCLEP LQVKFWFQNK RTQMKAQHER HENQILKSDN DKLRAENNRY  120
KEALSNATCP NCGGPAAIGE MSFDEQHLRI ENARLREEID RISAIAAKYV GKPVGSSFAP  180
LAIHGPSRSL ELEVGNFGNQ TGFVGDMYGT GDILRSVSIP SDTDKPMIVE LAVAAMEELV  240
RMAQSGDPLW VSTGNSMELL NEEEYFRTFP RGIGPKQLGL RTEASRESAV VIMNHINLVE  300
ILMDVNQWSC VFSGIVSRAL TLEVLSTGVA GNYNGALQVM TAEFQVPSPL VPTRENYFVR  360
YCKQHSDGSW AVVDVSLDSL RPNLISRTRR RPSGCLIQEL PNGYSKVTWI EHMEVDDRSV  420
HTMYKPLVHS GLAFGAKRWV STLERQCERL ASSMASNIPA SDLSVITSPE GRKSMLKLAE  480
RMVMSFCSGV GASTAHAWTT MSSTGSDDVR VMTRKSMDDP GRPPGIVLSA ATSFWIPVAP  540
KRVFDFLRDE NSRSEWDILS NGGMVQEMAH IANGREPGNC VSLLRVNSGN SSQSNMLILQ  600
ESCTDASGSY VIYAPVDIVA MNVVLSGGDP DYVALLPSGF AILPDGSVGG GDGNDQEVVS  660
SSNASGSCGS LLTVAFQILV DSVPTAKLSL GSVATVNSLI KCTVERIKAA LACDVGGGAP
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to ATML1. {ECO:0000269|PubMed:12505995}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3528680.0AK352868.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-14-J22.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009114536.10.0PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2
RefseqXP_009114537.10.0PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2
RefseqXP_013661998.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X1
RefseqXP_013661999.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X1
RefseqXP_013662000.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X2
RefseqXP_013662001.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X2
RefseqXP_018510478.10.0PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2
SwissprotQ93V990.0PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBLA0A3P5YKM20.0A0A3P5YKM2_BRACM; Uncharacterized protein
TrEMBLM4EL600.0M4EL60_BRARP; Uncharacterized protein
STRINGBra029527.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM49128149
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G04890.10.0protodermal factor 2
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]