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_01086.1_g00002.1
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: 849aa    MW: 93451.2 Da    PI: 5.9629
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_01086.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox54.22.5e-172684357
                             --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
                 Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                             k  ++t++q+e+Le+++ ++++ps  +r++L + +    +++ +q+kvWFqNrR ++k+
  Rsa1.0_01086.1_g00002.1 26 KYVRYTSDQVEALERVYSECPKPSSLRRQQLIRDCsilaHIEPKQIKVWFQNRRCRDKQ 84
                             5678****************************************************996 PP
2START157.97.7e-501633682202
                              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_01086.1_g00002.1 163 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQRCSGVAARACGLVSLEPV-KIAEILKDRPSWYRDCRSLEVYTMFPA 247
                              7899******************************************************.7777777777**************999 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_01086.1_g00002.1 248 GngGTIELVYMQTYAPTTLAPaRDFWTLRYTTSLDNGSYVVCERSLSGSGAGPNptsASQFVRAEMLSSGYLIRPCDGGGSIIHIV 333
                              999*******************************************9887777777899*************************** PP

                              E-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXX CS
                    START 168 ehvdlkgrlphwllrslvksglaegaktwvatlqr 202
                              +h +l++++++ +lr+l++s+ + ++k++ ++l++
  Rsa1.0_01086.1_g00002.1 334 DHLNLEAWSVPDVLRPLYESSKVVAQKMTISALRY 368
                              *****************************999987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007114.9162185IPR001356Homeobox domain
SuperFamilySSF466895.99E-162388IPR009057Homeodomain-like
SMARTSM003896.8E-152389IPR001356Homeobox domain
CDDcd000862.75E-142686No hitNo description
PfamPF000466.2E-152784IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.7E-172884IPR009057Homeodomain-like
CDDcd146865.67E-678117No hitNo description
PROSITE profilePS5084826.907153381IPR002913START domain
CDDcd088751.48E-66159373No hitNo description
SuperFamilySSF559612.47E-34162374No hitNo description
Gene3DG3DSA:3.30.530.201.3E-19162367IPR023393START-like domain
SMARTSM002341.0E-39162372IPR002913START domain
PfamPF018521.6E-47163369IPR002913START domain
PfamPF086701.3E-45696848IPR013978MEKHLA
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: 849 aa     Download sequence    Send to blast
MEMMEVANHL ERSSDRMNRH LDSNGKYVRY TSDQVEALER VYSECPKPSS LRRQQLIRDC  60
SILAHIEPKQ IKVWFQNRRC RDKQRKEASR LQSLNRKLSA MNKLLMEEND RLQKQVSQLV  120
CENGYMKQQL TTTVVNDASC DSVVNPPHHS LRDVNSPTGL ISIAEETLAE FLSKATGTAV  180
DWVQMPGMKP GPDSVGIFAI SQRCSGVAAR ACGLVSLEPV KIAEILKDRP SWYRDCRSLE  240
VYTMFPAGNG GTIELVYMQT YAPTTLAPAR DFWTLRYTTS LDNGSYVVCE RSLSGSGAGP  300
NPTSASQFVR AEMLSSGYLI RPCDGGGSII HIVDHLNLEA WSVPDVLRPL YESSKVVAQK  360
MTISALRYIR QLAQESNGEL VHGLGRQPAV LRTFSQRLSR GFNDAVNGFG DDGWSTMHCD  420
GAEDIIVAIN STKHLSNISS SLSFLGGVLC AKASMLLQNV PPAVLIQFLR EHRSEWADFH  480
VDAYSAATLK ADTFAYPVVR PTRFTGSQVI MPLGHTIEHE EMLEVVRLEG HSLAQEDGFM  540
SRDVHLLQIC TGIDENAVGA CSELIFAPIN EMFPDDAPLV PSGFRVIPID AKTGDVQDLI  600
TSNHRTLDLT SSLEVGPSPE NASGNCSSSS SSRCILTIAF QFPFEPNLQE NVAGMACQYV  660
RSVISSVQRV AMAISPSGIS SSLGSKLSPA SPEAVTLAQW ISQSYTHHLG SELVTIDSLG  720
SNDSVLKLIW DHQDAILCCT LKPQPVFMFA NQAGLDMLET TLVALQDITL EKIFDESGRK  780
ALCSDFAKLM QQGFACLSSG ICLSTMGRHV TYEQAIAWKV FASSDNKDDN SNNNNLHCLA  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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_01086.1_g00002.1
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
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
TrEMBLA0A1J3F1X70.0A0A1J3F1X7_NOCCA; Homeobox-leucine zipper protein REVOLUTA (Fragment)
TrEMBLA0A1J3F5L80.0A0A1J3F5L8_NOCCA; Homeobox-leucine zipper protein REVOLUTA (Fragment)
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]