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 XP_009114537.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family HD-ZIP
Protein Properties Length: 745aa    MW: 81598.2 Da    PI: 5.6455
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009114537.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.94.1e-1963118156
                     TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
        Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                     +++ +++t+ q++eLe++F+++++p+ ++r+eL++ l L+  qVk+WFqN+R+++k
  XP_009114537.1  63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRDLCLEPLQVKFWFQNKRTQMK 118
                     688999***********************************************998 PP
2START212.91.1e-662544731206
                     HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEE CS
           START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetle 83 
                     ela +a++elv++a+a++p+Wv+     + +n++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +     +a tle
  XP_009114537.1 254 ELAVAAMEELVRMAQAGDPLWVSTGnsmDLLNEEEYFRTFPRGIGpkplgLRTEASRESAVVIMNHINLVEILMDVN-QWSCVFSgivsRALTLE 347
                     57899******************9998999************999********************************.***************** PP

                     EECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE CS
           START  84 vissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvd 171
                     v+s+g      galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds +++     + R +++pSg+li++++ng+skvtw+eh++
  XP_009114537.1 348 VLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPNL----ISRTRRRPSGCLIQELPNGYSKVTWIEHME 438
                     ***********************************************************96....7999************************** PP

                     --SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
           START 172 lkgrlphwllrslvksglaegaktwvatlqrqcek 206
                     +++r++h ++++lv+sgla+gak+wv+tl+rqce+
  XP_009114537.1 439 VDDRSVHTMYKPLVHSGLAFGAKRWVSTLERQCER 473
                     *********************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.606.6E-2344118IPR009057Homeodomain-like
SuperFamilySSF466892.52E-1849120IPR009057Homeodomain-like
PROSITE profilePS5007116.42260120IPR001356Homeobox domain
SMARTSM003891.5E-1561124IPR001356Homeobox domain
PfamPF000461.0E-1663118IPR001356Homeobox domain
CDDcd000864.74E-1763121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084844.868245476IPR002913START domain
SuperFamilySSF559611.22E-35246475No hitNo description
CDDcd088752.16E-125249472No hitNo description
SMARTSM002341.5E-72254473IPR002913START domain
PfamPF018529.9E-56255473IPR002913START domain
Gene3DG3DSA:3.30.530.204.4E-5352472IPR023393START-like domain
SuperFamilySSF559611.44E-25493733No 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: 745 aa     Download sequence    Send to blast
MYHPSMFESH HMFDLTTKST SDNDLGITGS REDEFETKSG TEVTTDNPSG EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLC LEPLQVKFWF QNKRTQMKAQ  120
HERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENVRLRE  180
EIDRISAIAA KYVGKPVGSS FAPLGIHAPS RSLELEVGNF GNQTTGFVGD MYGTGDILRS  240
VSIPSDTDKP MIVELAVAAM EELVRMAQAG DPLWVSTGNS MDLLNEEEYF RTFPRGIGPK  300
PLGLRTEASR ESAVVIMNHI NLVEILMDVN QWSCVFSGIV SRALTLEVLS TGVAGNYNGA  360
LQVMTAEFQV PSPLVPTREN YFVRYCKQHS DGSWAVVDVS LDSLRPNLIS RTRRRPSGCL  420
IQELPNGYSK VTWIEHMEVD DRSVHTMYKP LVHSGLAFGA KRWVSTLERQ CERLASSMAS  480
NIPASDLSVI TSPEGRKSML KLAERMVMSF CSGVGASTAH AWTTMSSTGS DDVRVMTRKS  540
MDDPGRPPGI VLSAATSFWI PVAPKRVFDF LRDENSRSEW DILSNGGMVQ EMAHIANGRE  600
PGNCVSLLRV NSGNSSQSNM LILQESCTDA SGSYVIYAPV DIVAMNVVLS GGDPDYVALL  660
PSGFAILPDG SVGGGDGNDQ EVVSSSTTAS GSCGSLLTVA FQILVDSVPT AKLSLGSVAT  720
VNSLIKCTVE RIKAALACDV GGGAP
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Specifically expressed in the layer 1 (L1) of shoot meristems. {ECO:0000269|PubMed:12505995}.
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
PlantRegMapXP_009114537.1
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_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_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)
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]