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_009150087.1
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: 841aa    MW: 92515.5 Da    PI: 5.8665
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009150087.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox54.61.8e-172784457
                    -SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
        Homeobox  4 RttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                      ++t eq+e+Le+++ ++++p+  +r++L +++    +++ +q+kvWFqNrR ++k+
  XP_009150087.1 27 YVRYTGEQVEALERVYSECPKPTSLRRQQLIRECpflaNIEPKQIKVWFQNRRCRDKQ 84
                    6789***************************************************996 PP
2bZIP_1201.5e-06781231863
                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
          bZIP_1  18 rrsRqRKkaeieeLeekvkeLeaeNkaLkkeleelkkevaklksev 63 
                     rr+R + ++e  +L+   ++L+a Nk L +e+++l+k+v+ l se+
  XP_009150087.1  78 RRCRDKQRKEASRLQSVNQKLSAMNKLLMEENDRLQKQVSHLVSEN 123
                     9***************************************998887 PP
3START160.71.1e-501653722204
                     HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEE CS
           START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galqlm 94 
                     +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+ + g a+ra+g+v  ++++ ve+l d++  W ++++++e+      g  g+++l+
  XP_009150087.1 165 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQKCYGVAARACGLVSLEPMKIVEILKDRP-SWFRDCRSIEVFTMFPAGngGTIELI 258
                     68999*****************************************************9999999999.*************9999999****** 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+    +++vRae+lpSg+li+p+++g+s +++v+h++ +g++++ +lr+l+
  XP_009150087.1 259 YMQTYAPTTLAPaRDFWTLRYTTSLEKGSFVVCERSLSGSGAGPNatsAAQFVRAEMLPSGYLIRPCDGGGSIIHIVDHINFEGWSVPDVLRPLY 353
                     **************************************999999889999********************************************* PP

                     HHHHHHHHHHHHHHTXXXX CS
           START 186 ksglaegaktwvatlqrqc 204
                     +s+ + +++++ a+l++ +
  XP_009150087.1 354 ESSKVVAQRMTIAALRYVR 372
                     ***************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007115.1432185IPR001356Homeobox domain
SuperFamilySSF466896.42E-162388IPR009057Homeodomain-like
SMARTSM003891.4E-132389IPR001356Homeobox domain
CDDcd000863.87E-152686No hitNo description
PfamPF000465.8E-152784IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.607.1E-182884IPR009057Homeodomain-like
CDDcd146862.05E-678117No hitNo description
PROSITE profilePS5084827.152155383IPR002913START domain
CDDcd088758.92E-70159373No hitNo description
Gene3DG3DSA:3.30.530.201.7E-19162355IPR023393START-like domain
SMARTSM002346.0E-42164374IPR002913START domain
PfamPF018523.0E-48165372IPR002913START domain
SuperFamilySSF559612.33E-34165374No hitNo description
PfamPF086702.1E-48693840IPR013978MEKHLA
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: 841 aa     Download sequence    Send to blast
MAMTVAVGNR HESGENINRH LDSSGKYVRY TGEQVEALER VYSECPKPTS LRRQQLIREC  60
PFLANIEPKQ IKVWFQNRRC RDKQRKEASR LQSVNQKLSA MNKLLMEEND RLQKQVSHLV  120
SENGYMKQQL TLTTLGTDAS CDSVDPTPPQ HPLRDANSPA GLMAIAEETL AEFLSKATGT  180
AVDWVQMPGM KPGPDSVGIF AISQKCYGVA ARACGLVSLE PMKIVEILKD RPSWFRDCRS  240
IEVFTMFPAG NGGTIELIYM QTYAPTTLAP ARDFWTLRYT TSLEKGSFVV CERSLSGSGA  300
GPNATSAAQF VRAEMLPSGY LIRPCDGGGS IIHIVDHINF EGWSVPDVLR PLYESSKVVA  360
QRMTIAALRY VRQVAHETNG EVVYGLGRQP AVLRTFSQRL SRGFNDAVNG FNDDGWSIMH  420
CNGAEDITVA VNSTKHLNSF SDPLSFLGGV LCAKASMLLQ NVCPAVLVRF LREHRSEWAD  480
FNVDAYSAAT LKAGAFAYSG MRPTTFTGSQ IIMPLGNTIE KEEMLEVVRL EGHSLVPEDS  540
FLSRDVHLLQ ICTGVDEDAV GACSELVFAP VNEMFPDDAP LVPSGFRVIP VDSKTGDAQD  600
LLTANHRTLD LTSSQDVGST PETGSSPSSR CILTIAFQFP FENNLQENVA NMACQYVRSV  660
ISSVQRVAVA LSPSGLIQIP GSKLSPGSPE AVSLAIWICQ SYKQHFGSDL LRTDSLGGDA  720
LLRQLWDHQD AILCCSLKPQ PVFMFANQAG LDMLETTLVA LQDIALEKIF DESGRKALCP  780
DFAKLMQQGF ACLPSGMCVS TMGRHVSYEQ AVSWKVFSDC EDNNNNRLHC LAFLFANWSF  840
L
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_009150087.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009150087.10.0PREDICTED: homeobox-leucine zipper protein REVOLUTA-like isoform X1
RefseqXP_013642495.10.0homeobox-leucine zipper protein REVOLUTA-like isoform X1
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]