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_00915.1_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: 851aa    MW: 93149.8 Da    PI: 5.9295
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00915.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox56.45.1e-182583357
                             --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
                 Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                             k  ++t+eq+e+Le++++++++ps  +r++L +++    +++ +q+kvWFqNrR ++k+
  Rsa1.0_00915.1_g00001.1 25 KYVRYTAEQVEALERVYAECPKPSSLRRQQLIRECsilaNIEPKQIKVWFQNRRCRDKQ 83
                             56789***************************************************996 PP
2START153.12.3e-481623672202
                              HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECT CS
                    START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetleviss 87 
                              +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+ +sg a+ra+g+v  +++   +e+l+d++ W +++++ e+      
  Rsa1.0_00915.1_g00001.1 162 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQRCSGVAARACGLVSLEPV-KIAEILKDRPAWFRDCRSLEVFTMFPA 246
                              7899******************************************************.7777777777***********999999 PP

                              T..EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEE CS
                    START  88 g..galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwv 167
                              g  g+++l +++++a+++l+p Rdf+++Ry+ +l  g++v++++S++     p+    s++vRae+l Sg+li+p+++g+s +++v
  Rsa1.0_00915.1_g00001.1 247 GngGTIELVYMQTYAPTTLAPaRDFWTLRYTTSLDNGSFVVCERSLSGSGAGPNaasASQFVRAEMLSSGYLIRPCDGGGSIIHIV 332
                              999********************************************999999989999*************************** PP

                              E-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXX CS
                    START 168 ehvdlkgrlphwllrslvksglaegaktwvatlqr 202
                              +h +l++++++ +lr+l++s+ + ++k++ ++l++
  Rsa1.0_00915.1_g00001.1 333 DHLNLEAWSVPDVLRPLYESSKVVAQKMTISALRY 367
                              *****************************999987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007115.3052084IPR001356Homeobox domain
SuperFamilySSF466891.11E-162187IPR009057Homeodomain-like
SMARTSM003892.0E-162288IPR001356Homeobox domain
CDDcd000866.32E-162585No hitNo description
PfamPF000461.3E-152683IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.1E-182783IPR009057Homeodomain-like
CDDcd146863.30E-677116No hitNo description
PROSITE profilePS5084826.98152380IPR002913START domain
CDDcd088753.47E-67156372No hitNo description
SuperFamilySSF559612.2E-34161373No hitNo description
SMARTSM002341.6E-37161371IPR002913START domain
Gene3DG3DSA:3.30.530.205.7E-19161366IPR023393START-like domain
PfamPF018524.9E-46162368IPR002913START domain
PfamPF086701.3E-45695850IPR013978MEKHLA
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009855Biological Processdetermination of bilateral symmetry
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0009956Biological Processradial pattern formation
GO:0010014Biological Processmeristem initiation
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010089Biological Processxylem development
GO:0030154Biological Processcell differentiation
GO:0005634Cellular Componentnucleus
GO:0008289Molecular Functionlipid binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 851 aa     Download sequence    Send to blast
MEMAVANHRE RSSDSMNRHL DSSGKYVRYT AEQVEALERV YAECPKPSSL RRQQLIRECS  60
ILANIEPKQI KVWFQNRRCR DKQRKEASRL QSVNRKLSAM NKLLMEENDR LQKQVSQLVC  120
ENGYMKQQLT TTVVNDPSCD SVVTTPQHSL RDANSPAGLL SIAEETLAEF LSKATGTAVD  180
WVQMPGMKPG PDSVGIFAIS QRCSGVAARA CGLVSLEPVK IAEILKDRPA WFRDCRSLEV  240
FTMFPAGNGG TIELVYMQTY APTTLAPARD FWTLRYTTSL DNGSFVVCER SLSGSGAGPN  300
AASASQFVRA EMLSSGYLIR PCDGGGSIIH IVDHLNLEAW SVPDVLRPLY ESSKVVAQKM  360
TISALRYIRQ LAQESNGELV YGLGRQPAVL RTFSQRLSRG FNDAVNGFGD DGWSTMHCDG  420
AEDIIVAINS TKHLNNMSNS LSFLGGVLCA KASMLLQNVP PAVLIRFLRE HRSEWADFNV  480
DAYSAATLKA GSFAYPGMRP TRFTGSQIIM PLGHTIEHEE MLEVVRLEGH SLAQEDAFMS  540
RDVHLLQICT GIDENAVGAC SELIFAPINE MFPDDAPLVP SGFRVIPVDA KTGDAQDLLT  600
ANHRTLDLTS SLEVGPSPEN ASGNSSSGSN SRCILTIAFQ FPFENNLQDN VAGMACQYVR  660
SVISSVQRVA MAISPSGISP SLGSKLSPGS PEAVTLAQWI SQSYTHHLGS ELLTVDSLGS  720
NDSVLKLLWD HQDAILCCSL KPQPVFMFAN QAGLDMLETT LVALQDITLE KIFDESGRKA  780
LCSDFAKLMQ QGYACLPSGI CLSTMGRHVT YEQAVAWKVF AATTASSENN SDGNDHTLHC  840
LAFSFVNWSF V
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the regulation of interfascicular fiber (cortical cells) and secondary xylem differentiation in the inflorescence stems. Required for lateral shoot meristems (LSMs) and flower meristems (FMs) initiation. May be involved in the determination of vascular patterning and organ polarity (PubMed:10559440, PubMed:11169198, PubMed:11402186, PubMed:15111711, PubMed:15598805, PubMed:7555701). Directly regulates the expression of AGO10, ZPR1, ZPR2, ZPR3 and ZPR4 (PubMed:22781836). Required to regulate adaxial-abaxial polarity and leaf axial patterning (PubMed:20807212). {ECO:0000269|PubMed:10559440, ECO:0000269|PubMed:11169198, ECO:0000269|PubMed:11402186, ECO:0000269|PubMed:15111711, ECO:0000269|PubMed:15598805, ECO:0000269|PubMed:20807212, ECO:0000269|PubMed:22781836, ECO:0000269|PubMed:7555701}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00915.1_g00001.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. Repressed by ZPR and miR165. Induced by DOF5.1 (PubMed:20807212). {ECO:0000269|PubMed:15111711, ECO:0000269|PubMed:17237362, ECO:0000269|PubMed:20807212}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1889940.0AF188994.1 Arabidopsis thaliana homeodomain-leucine zipper protein interfascicular fiberless 1 (IFL1) mRNA, complete cds.
GenBankAF2335920.0AF233592.1 Arabidopsis thaliana REVOLUTA mRNA, complete cds.
GenBankAK2295640.0AK229564.1 Arabidopsis thaliana mRNA for REVOLUTA or interfascicular fiberless 1, complete cds, clone: RAFL19-08-C22.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018446535.10.0PREDICTED: homeobox-leucine zipper protein REVOLUTA
RefseqXP_018446536.10.0PREDICTED: homeobox-leucine zipper protein REVOLUTA
SwissprotQ9SE430.0REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBLA0A3P6CRT20.0A0A3P6CRT2_BRACM; Uncharacterized protein
TrEMBLM4CE270.0M4CE27_BRARP; Uncharacterized protein
STRINGBra002458.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM47792754
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60690.10.0HD-ZIP family protein
Publications ? help Back to Top
  1. Lian H,Li X,Liu Z,He Y
    HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis.
    J. Exp. Bot., 2013. 64(11): p. 3397-410
    [PMID:23918970]
  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]
  3. Baima S, et al.
    Negative feedback regulation of auxin signaling by ATHB8/ACL5-BUD2 transcription module.
    Mol Plant, 2014. 7(6): p. 1006-1025
    [PMID:24777988]
  4. Jia X, et al.
    Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic.
    Plant Sci., 2015. 233: p. 11-21
    [PMID:25711809]
  5. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  6. Shi B, et al.
    Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis.
    PLoS Genet., 2016. 12(7): p. e1006168
    [PMID:27398935]