PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC142_p8
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: 849aa    MW: 92755.5 Da    PI: 5.7178
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC142_p8genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox253.2e-082571345
               --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHH CS
   Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVk 45
               k  ++t+eq+e+Le++++++++ps  +r++L +++    +++ +q+k
  RrC142_p8 25 KYVRYTAEQVEALERVYAECPKPSSLRRQQLIRECsilaNIEPKQIK 71
               56789******************************999999999997 PP
2START153.12.3e-481503552202
                HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEEEEXXT CS
      START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galqlmvaelq 99 
                +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+ +sg a+ra+g+v  +++   +e+l+d++ W +++++ e+      g  g+++l +++++
  RrC142_p8 150 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQRCSGVAARACGLVSLEPV-KIAEILKDRPAWFRDCRSLEVFTMFPAGngGTIELVYMQTY 248
                7899******************************************************.7777777777***********999999999*********** PP

                TXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHH CS
      START 100 alsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrslvksglaegakt 195
                a+++l+p Rdf+++Ry+ +l  g++v++++S++     p+    s++vRae+l Sg+li+p+++g+s +++v+h +l++++++ +lr+l++s+ + ++k+
  RrC142_p8 249 APTTLAPaRDFWTLRYTTSLDNGSFVVCERSLSGSGAGPNaasASQFVRAEMLSSGYLIRPCDGGGSIIHIVDHLNLEAWSVPDVLRPLYESSKVVAQKM 348
                *********************************999999989999******************************************************* PP

                HHHHTXX CS
      START 196 wvatlqr 202
                + ++l++
  RrC142_p8 349 TISALRY 355
                *999987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466892.06E-62170IPR009057Homeodomain-like
CDDcd000861.87E-62571No hitNo description
PfamPF000467.7E-62671IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.602.4E-72771IPR009057Homeodomain-like
PROSITE profilePS5084826.98140368IPR002913START domain
CDDcd088753.56E-67144360No hitNo description
Gene3DG3DSA:3.30.530.205.7E-19149354IPR023393START-like domain
SMARTSM002341.6E-37149359IPR002913START domain
SuperFamilySSF559612.2E-34149361No hitNo description
PfamPF018524.9E-46150356IPR002913START domain
PfamPF086701.2E-28711848IPR013978MEKHLA
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: 849 aa     Download sequence    Send to blast
MEMAVANHRE RSSDSMNRHL DSSGKYVRYT AEQVEALERV YAECPKPSSL RRQQLIRECS  60
ILANIEPKQI KRKEASRLQS VNRKLSAMNK LLMEENDRLQ KQVSQLVCEN GYMKQQLTTT  120
VVNDPSCDSV VTTPQHSLRD ANSPAGLLSI AEETLAEFLS KATGTAVDWV QMPGMKPGPD  180
SVGIFAISQR CSGVAARACG LVSLEPVKIA EILKDRPAWF RDCRSLEVFT MFPAGNGGTI  240
ELVYMQTYAP TTLAPARDFW TLRYTTSLDN GSFVVCERSL SGSGAGPNAA SASQFVRAEM  300
LSSGYLIRPC DGGGSIIHIV DHLNLEAWSV PDVLRPLYES SKVVAQKMTI SALRYIRQLA  360
QESNGELVYG LGRQPAVLRT FSQRLSRGFN DAVNGFGDDG WSTMHCDGAE DIIVAINSTK  420
HLNNMSNSLS FLGGVLCAKA SMLLQNVPPA VLIRFLREHR SEWADFNVDA YSAATLKAGS  480
FAYPGMRPTR FTGSQIIMPL GHTIEHEEML EVVRLEGHSL AQEDAFMSRD VHLLQICTGI  540
DENAVGACSE LIFAPINEMF PDDAPLVPSG FRVIPVDAKT VMIFLLLNDI ACVSRLTFLF  600
MFCFHSKQGD AQDLLTANHR TLDLTSSLEV GPSPENASGN SSSGSNSRCI LTIAFQFPFE  660
NNLQDNVAGM ACQYVRSVIS SVQRVAMAIS PSGISPSLGS KLSPGSPEAV TLAQWISQSY  720
THHLGSELLT VDSLGSNDSP QPVFMFANQA GLDMLETTLV ALQDITLEKI FDESGRKALC  780
SDFAKLMQQG YACLPSGICL STMGRHVTYE QAVAWKVFAA TTASSENNSD GNDHTLHSLA  840
FSFVNWSFV
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 -- 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]