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 XP_009120606.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family HD-ZIP
Protein Properties Length: 850aa    MW: 93038.7 Da    PI: 5.8455
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009120606.1genomeNCBIView 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+
  XP_009120606.1 25 KYVRYTAEQVEALERVYAECPKPSSLRRQQLIRECsilaNIEPKQIKVWFQNRRCRDKQ 83
                    56789***************************************************996 PP
2START153.91.3e-481623672202
                     HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEE CS
           START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galqlm 94 
                     +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+ +sg a+ra+g+v  +++   +e+l+d++ W +++++ e+      g  g+++l 
  XP_009120606.1 162 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQRCSGVAARACGLVSLEPV-KIAEILKDRPSWFRDCRSLEVFTMFPAGngGTIELV 255
                     7899******************************************************.7777777777***********999999999****** PP

                     EEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHHHH CS
           START  95 vaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrslv 185
                     +++++a+++l+p Rdf+++Ry+ +l  g++v++++S++     p+    s++vRae+l Sg+li+p+++g+s +++v+h +l++++++ +lr+l+
  XP_009120606.1 256 YMQTYAPTTLAPaRDFWTLRYTTSLDNGSFVVCERSLSGSGAGPNaasASQFVRAEMLSSGYLIRPCDGGGSIIHIVDHLNLEAWSVPDVLRPLY 350
                     **************************************999999989999********************************************* PP

                     HHHHHHHHHHHHHHTXX CS
           START 186 ksglaegaktwvatlqr 202
                     +s+ + ++k++ ++l++
  XP_009120606.1 351 ESSKVVAQKMTISALRY 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
CDDcd000866.31E-162585No hitNo description
PfamPF000461.3E-152683IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.0E-182783IPR009057Homeodomain-like
CDDcd146863.29E-677116No hitNo description
PROSITE profilePS5084827.127152380IPR002913START domain
CDDcd088758.27E-68156372No hitNo description
SuperFamilySSF559611.14E-34161373No hitNo description
SMARTSM002344.7E-38161371IPR002913START domain
Gene3DG3DSA:3.30.530.202.7E-19161366IPR023393START-like domain
PfamPF018522.9E-46162368IPR002913START domain
PfamPF086704.0E-46695849IPR013978MEKHLA
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: 850 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 IAEILKDRPS 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 SLEVGPTPEN ASGNSSSSSS SRCILTIAFQ FPFENNLQDN VAGMACQYVR  660
SVISSVQRVA MAISPSGISP SLGSKLSPGS PEAVTLAQWI SQSYTHHLGS ELLTVDSLGS  720
NDSVLKLLWD HQDAILCCSL KPQPVFMFAN QAGLDMLETT LVALQDITLE KIFDESGRKA  780
LCSDFAKLMQ QGYACLPSGI CLSTMGRHVT YEQAVAWKVF APAAASSENN DGNDNTLHCL  840
AFSFVNWSFV
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed at the earliest stages and throughout LSM initiation and development. In embryo development, expressed at the heart stage until the 'walking stick' stage in the adaxial portion of the cotyledon primordia, the shoot apical meristem (SAM) and the vascular precursor cells of the hypocotyl and root. In developing flowers, expressed first at stage 1 in the center of L3 layer and then expands to the center of L2 and L1 layers. Expressed in the center of flower meristem through stages 4 and 5. At stage 6, expressed in the adaxial side of the carpel primordia and then on the adaxial carpel face. {ECO:0000269|PubMed:11169198}.
UniprotTISSUE SPECIFICITY: Expressed in the interfascicular regions of stem and vascular bundles of young roots and leaves. {ECO:0000269|PubMed:10559440}.
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
PlantRegMapXP_009120606.1
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_009120605.10.0PREDICTED: homeobox-leucine zipper protein REVOLUTA
RefseqXP_009120606.10.0PREDICTED: 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)
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]