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 Rsa1.0_02611.1_g00001.1
Organism
Raphanus sativus
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: 743aa    MW: 81430 Da    PI: 5.6478
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02611.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.42.8e-1963118156
                              TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
                 Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                              +++ +++t+ q++eLe++F+++++p+ ++r+eL++ l L+  qVk+WFqN+R+++k
  Rsa1.0_02611.1_g00001.1  63 KKRYHRHTQRQIQELEAFFKECPHPDDKQRKELSRDLCLEPLQVKFWFQNKRTQMK 118
                              688999***********************************************998 PP
2START2131.1e-662534721206
                              HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S. CS
                    START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla. 77 
                              ela +a++elv++a++++p+Wv+     e +n++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +  
  Rsa1.0_02611.1_g00001.1 253 ELAVAAMEELVRMAQSGDPLWVSTGnsmELLNEEEYFRTFPRGIGpkqlgLRTEASRESAVVIMNHINLVEILMDVN-QWSCVFSg 337
                              57899******************9998899************999********************************.******** PP

                              ...EEEEEEEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEE CS
                    START  78 ...kaetlevissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgil 153
                                 +a tlev+s+g      galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds +++     + R +++pSg+l
  Rsa1.0_02611.1_g00001.1 338 ivsRALTLEVLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPNL----ISRTRRRPSGCL 419
                              ********************************************************************96....7999******** PP

                              EEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                    START 154 iepksnghskvtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                              i++++ng+skvtw+eh+++++r++h ++++lv+sgla+gak+wv+tl+rqce+
  Rsa1.0_02611.1_g00001.1 420 IQELPNGYSKVTWIEHMEVDDRSVHTMYKPLVHSGLAFGAKRWVSTLERQCER 472
                              ***************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.602.9E-2341118IPR009057Homeodomain-like
SuperFamilySSF466893.01E-1850120IPR009057Homeodomain-like
PROSITE profilePS5007116.3960120IPR001356Homeobox domain
SMARTSM003896.7E-1661124IPR001356Homeobox domain
PfamPF000467.3E-1763118IPR001356Homeobox domain
CDDcd000863.36E-1763121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084845.039244475IPR002913START domain
SuperFamilySSF559611.65E-35245474No hitNo description
CDDcd088754.25E-125248471No hitNo description
SMARTSM002349.7E-73253472IPR002913START domain
PfamPF018529.5E-56254472IPR002913START domain
Gene3DG3DSA:3.30.530.204.3E-5350471IPR023393START-like domain
SuperFamilySSF559611.37E-25492731No 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: 743 aa     Download sequence    Send to blast
MYHPSMFESH HMFDMTTKST SDNDLGITGS REDEFETKSG TEATTENPSG EELQDPNQRP  60
NKKKRYHRHT QRQIQELEAF FKECPHPDDK QRKELSRDLC LEPLQVKFWF QNKRTQMKAQ  120
HERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE  180
EIDRISAIAA KYVGKPVGSS FAPLAIHGPS RSLELEVGNF GNQTGFVGDM YGTGDILRSV  240
SIPSDTDKPM IVELAVAAME ELVRMAQSGD PLWVSTGNSM ELLNEEEYFR TFPRGIGPKQ  300
LGLRTEASRE SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST GVAGNYNGAL  360
QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL DSLRPNLISR TRRRPSGCLI  420
QELPNGYSKV TWIEHMEVDD RSVHTMYKPL VHSGLAFGAK RWVSTLERQC ERLASSMASN  480
IPASDLSVIT SPEGRKSMLK LAERMVMSFC SGVGASTAHA WTTMSSTGSD DVRVMTRKSM  540
DDPGRPPGIV LSAATSFWIP VAPKRVFDFL RDENSRSEWD ILSNGGMVQE MAHIANGREP  600
GNCVSLLRVN SGNSSQSNML ILQESCTDAS GSYVIYAPVD IVAMNVVLSG GDPDYVALLP  660
SGFAILPDGS VGGGDGNDQE VVSSSNASGS CGSLLTVAFQ ILVDSVPTAK LSLGSVATVN  720
SLIKCTVERI KAALACDVGG GAP
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_02611.1_g00001.1
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_013662000.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X2
RefseqXP_013662001.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X2
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]