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 RrC3602_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: 840aa    MW: 92044.6 Da    PI: 6.2093
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC3602_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox54.81.6e-172583357
                --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
    Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                k  ++t+eq+e+Le+++ ++++p+  +r++L +++    +++ +q+kvWFqNrR ++k+
  RrC3602_p1 25 KYVRYTAEQVEALERVYSECPKPTSLRRQQLISECpilaHIEPKQIKVWFQNRRCRDKQ 83
                56789***************************************************996 PP
2START163.81.3e-511623692204
                 HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEEEEXX CS
       START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galqlmvael 98 
                 +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+ ++g a+ra+g+v  ++++ ve+l d++  W +++++ e+      g  g+++l+++++
  RrC3602_p1 162 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQKCNGVAARACGLVSLEPMKIVEILKDRP-SWFRDCRSLEVFTMFPAGngGTIELIYMQT 259
                 68999*****************************************************9999999999.***********999999999********** PP

                 TTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHH CS
       START  99 qalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrslvksglaega 193
                 +a+++l+p Rdf+++Ry+ +l  g++v++++S++     p+   s+++vRae+lpSg+li+p+++g+s +++v+h++l+g++++ +lr+l++s+ + ++
  RrC3602_p1 260 YAPTTLAPaRDFWTLRYTTSLDNGSFVVCERSLSGSGAGPNansSAQFVRAEMLPSGYLIRPCDGGGSIIHIVDHINLEGWSVPDVLRPLYESSKVVAQ 358
                 **********************************988888888899***************************************************** PP

                 HHHHHHTXXXX CS
       START 194 ktwvatlqrqc 204
                 +++ a+l++ +
  RrC3602_p1 359 RMTIAALRHIK 369
                 ******99865 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007114.8842084IPR001356Homeobox domain
SuperFamilySSF466895.56E-162287IPR009057Homeodomain-like
SMARTSM003891.6E-142288IPR001356Homeobox domain
CDDcd000861.32E-142585No hitNo description
PfamPF000465.2E-152683IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.3E-172783IPR009057Homeodomain-like
PROSITE profilePS5084827.054152371IPR002913START domain
CDDcd088754.05E-70156370No hitNo description
Gene3DG3DSA:3.30.530.205.4E-21160365IPR023393START-like domain
SMARTSM002341.2E-42161371IPR002913START domain
SuperFamilySSF559612.06E-35162372No hitNo description
PfamPF018523.6E-49162369IPR002913START domain
PfamPF086705.0E-47692839IPR013978MEKHLA
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0008289Molecular Functionlipid binding
Sequence ? help Back to Top
Protein Sequence    Length: 840 aa     Download sequence    Send to blast
MAMAVANHNE SGGDNINRHL DSSGKYVRYT AEQVEALERV YSECPKPTSL RRQQLISECP  60
ILAHIEPKQI KVWFQNRRCR DKQRKEASRL LSVNQKLSAM NKLLMEENDR LQKQVSHLVT  120
ENGYMKQQLT TTVGADASCD SVDPTPHHSL RDANSPAGLL AIAEETLAEF LSKATGTAVD  180
WVQMPGMKPG PDSVGIFAIS QKCNGVAARA CGLVSLEPMK IVEILKDRPS WFRDCRSLEV  240
FTMFPAGNGG TIELIYMQTY APTTLAPARD FWTLRYTTSL DNGSFVVCER SLSGSGAGPN  300
ANSSAQFVRA EMLPSGYLIR PCDGGGSIIH IVDHINLEGW SVPDVLRPLY ESSKVVAQRM  360
TIAALRHIKQ VAHERNGEVV YGLGRQPAIL RTFSQRLSRG FNDAVNGFND DGWSIAHCNG  420
AEDITVAVNS TKHLNRFSDS LSFLGGVLCA KASMLLQNVS PAVLIRFLRE HRSEWADFNV  480
DAYSAATLKA GAFAYSGIRS TAFTGSQIIM PLGNTIEKEE MLEVVRLEGH SLVQEYTSLS  540
RDVHLLQICT GVDEDAVGAC SELIFAPINE MFPDDAPLVP SGFRVIPLDS KTGDAQDLLT  600
ANHRTLDSTS SQYVGSTTSE TGSNPSTRCI LTIAFQFPFE NNLQENVANM ACQYLRSVIS  660
SVQRVAVALS PSSGLNPVPG SKLPPGSPEA VTLAIWISQS YRQQFGSDLL RTDSLGGDSL  720
LRQLWDHQDA ILCCSLKPQP VFMFANQAGL DMLETTLVAI QDITLEKIFD ESGRKALCPD  780
FAKLMQQGFA CLPSGMCVST MGRHVSYEQA VAWKVFANCE GNNNNGIHCL AFLFANWSFL
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}.
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018434000.10.0PREDICTED: homeobox-leucine zipper protein REVOLUTA-like
SwissprotQ9SE430.0REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBLA0A3P5Z0W90.0A0A3P5Z0W9_BRACM; Uncharacterized protein
STRINGBra038295.1-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]