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 RrC5949_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: 801aa    MW: 88210.6 Da    PI: 6.3912
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC5949_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox54.32.2e-172684357
                --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
    Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                k  ++t++q+e+Le+++ ++++ps  +r++L + +    +++ +q+kvWFqNrR ++k+
  RrC5949_p1 26 KYVRYTSDQVEVLERVYSECPKPSSLRRQQLIRDCsilaHIEPKQIKVWFQNRRCRDKQ 84
                5678****************************************************996 PP
2START158.65e-501633682202
                 HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEEEEXX CS
       START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galqlmvael 98 
                 +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+ +sg a+ra+g+v  +++   +e+l+d++ W +++++ e++     g  g+++l ++++
  RrC5949_p1 163 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQRCSGVAARACGLVSLEPV-KIAEILKDRPSWYRDCRSLEVYTIFPAGngGTIELVYMQT 260
                 7899******************************************************.7777777777*******9999999999999********** 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+l Sg+li+p+++g+s +++v+h +l++++++ +lr+l++s+ + ++
  RrC5949_p1 261 YAPTTLAPaRDFWTLRYTTSLDNGSYVVCERSLSGSGAGPNptsASQFVRAEMLSSGYLIRPCDGGGSIIHIVDHLNLEAWSVPDVLRPLYESSKVVAQ 359
                 *********************************9887777777899***************************************************** PP

                 HHHHHHTXX CS
       START 194 ktwvatlqr 202
                 k++ ++l++
  RrC5949_p1 360 KMTISALRY 368
                 ***999987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007114.8842185IPR001356Homeobox domain
SMARTSM003895.1E-152389IPR001356Homeobox domain
SuperFamilySSF466895.13E-162388IPR009057Homeodomain-like
CDDcd000861.95E-142686No hitNo description
PfamPF000465.3E-152784IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.602.0E-172881IPR009057Homeodomain-like
CDDcd146865.27E-678117No hitNo description
Gene3DG3DSA:1.20.5.1706.7E-482131No hitNo description
PROSITE profilePS5084827.152153381IPR002913START domain
CDDcd088754.35E-67159373No hitNo description
Gene3DG3DSA:3.30.530.202.7E-19162367IPR023393START-like domain
SMARTSM002342.9E-40162372IPR002913START domain
SuperFamilySSF559613.16E-34162374No hitNo description
PfamPF018521.0E-47163369IPR002913START domain
PfamPF086709.2E-23696772IPR013978MEKHLA
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: 801 aa     Download sequence    Send to blast
MEMMEVANHL ERSSDRMNRH LDSNGKYVRY TSDQVEVLER VYSECPKPSS LRRQQLIRDC  60
SILAHIEPKQ IKVWFQNRRC RDKQRKEASR LQSLNRKLSA MNKLLMEEND RLQKQVSQLV  120
RENEYMKQQL TTTVVNDARC DSVVTTPHHS LRDANSPTGL ISIAEETLAE FLSKATGTAV  180
DWVQMPGMKP GPDSVGIFAI SQRCSGVAAR ACGLVSLEPV KIAEILKDRP SWYRDCRSLE  240
VYTIFPAGNG GTIELVYMQT YAPTTLAPAR DFWTLRYTTS LDNGSYVVCE RSLSGSGAGP  300
NPTSASQFVR AEMLSSGYLI RPCDGGGSII HIVDHLNLEA WSVPDVLRPL YESSKVVAQK  360
MTISALRYIR QLAQESNGEL VHGLGRQPAV LRTFSQRLSR GFNDAVNGFG DDGWSTMHCD  420
GAEDIIVAIN STKHLSNISS SLSFLGGVLC AKASMLLHNV PPAVLIQFLR EHRSEWADFH  480
VDAYSAATLK ADTFAYPVVR PTRFTGSQVI MPLGHTIEHE EMLEVVRLEG HSLAQEDGFM  540
SRDVHLLQIC TGIDQNAVGA CSELIFAPIN EMFSDDAPLV PSGFRVIPID AKTGDVQDLI  600
TSNHRTLDLT SSLEVGRSPE NASGNCSSSS SSRCILTIAF QFPFEPNLQE NVAGMACQYV  660
RSVISSVQRV AMAISPSGIS SSLGSKLSPA SPEAVTLAQW ISQSYTHHLG SELVTSDSLG  720
SNDSVLKLIW NHQDAILCCT LKPQPVFMFA NQAGLDMLET TLVALQDITL DELLLGKCLL  780
PPTTRTTTVI IVICIVLLSR L
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
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_018454374.10.0PREDICTED: homeobox-leucine zipper protein REVOLUTA-like
SwissprotQ9SE430.0REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBLA0A078H2900.0A0A078H290_BRANA; BnaA10g13520D protein
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]