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 Ciclev10027790m
Common NameCICLE_v10027790mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family HD-ZIP
Protein Properties Length: 886aa    MW: 97481.3 Da    PI: 5.765
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10027790mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox41.32.6e-132982352
                     --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHH CS
         Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrR 52
                     k  ++t+eq+e+Le+++ ++++ps  +r++L +++    +++ +q+kvWFq  +
  Ciclev10027790m 29 KYVRYTAEQVEALERVYSECPKPSSLRRQQLIRECpilsNIEPKQIKVWFQRSK 82
                     5679***********************************************765 PP
2START1593.6e-502064142205
                      HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEE CS
            START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galql 93 
                      +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+++sg a+ra+g+v  +++   +e+l+d++ W +++++ e+      g  g+++l
  Ciclev10027790m 206 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQSCSGVAARACGLVSLEPT-KIAEILKDRPSWFRDCRSLEVFTMFPAGnaGTIEL 298
                      7899******************************************************.7777777777*****************99****** PP

                      EEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHH CS
            START  94 mvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrs 183
                       +++ +a+++l+p Rdf+++Ry+ +l  g++v++++S++     p+    +++vRae+lpSg+li+p+++g+s +++v+h +l++++++++lr+
  Ciclev10027790m 299 LYTQAYAPTTLAPaRDFWTLRYTTTLDNGSLVVCERSLSGSGAGPNpasAAQFVRAEMLPSGCLIRPCDGGGSIIHIVDHLNLEAWSVPEVLRP 392
                      ***************************************988888878999******************************************* PP

                      HHHHHHHHHHHHHHHHTXXXXX CS
            START 184 lvksglaegaktwvatlqrqce 205
                      l++s+ + +++++ a+l++ ++
  Ciclev10027790m 393 LYESSKVVAQRMTIAALRYVRQ 414
                      *****************98765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.604.3E-13679IPR009057Homeodomain-like
PROSITE profilePS5007112.052488IPR001356Homeobox domain
SMARTSM003893.0E-52692IPR001356Homeobox domain
SuperFamilySSF466891.03E-102786IPR009057Homeodomain-like
CDDcd000861.16E-102986No hitNo description
PfamPF000467.9E-113082IPR001356Homeobox domain
CDDcd146863.01E-6111159No hitNo description
PROSITE profilePS5084826.956196424IPR002913START domain
CDDcd088754.75E-71200416No hitNo description
SMARTSM002344.8E-41205415IPR002913START domain
Gene3DG3DSA:3.30.530.207.7E-19205392IPR023393START-like domain
SuperFamilySSF559612.61E-32205417No hitNo description
PfamPF018521.2E-47206414IPR002913START domain
PfamPF086701.1E-50741884IPR013978MEKHLA
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: 886 aa     Download sequence    Send to blast
MAMVIQQQQQ QQRESSSGSI NKHQLDNGKY VRYTAEQVEA LERVYSECPK PSSLRRQQLI  60
RECPILSNIE PKQIKVWFQR SKKCYRLAED FVDEELCMWE ERLDFLNWDL NRILAVVLIR  120
MCREKQRKEA SRLQTVNRKL TAMNKLLMEE NDRLQKQVSQ LVCENGYMKQ QLRTAPATTD  180
ASCDSVVTTP QHSLRDANNP AGLLSIAEET LAEFLSKATG TAVDWVQMPG MKPGPDSVGI  240
FAISQSCSGV AARACGLVSL EPTKIAEILK DRPSWFRDCR SLEVFTMFPA GNAGTIELLY  300
TQAYAPTTLA PARDFWTLRY TTTLDNGSLV VCERSLSGSG AGPNPASAAQ FVRAEMLPSG  360
CLIRPCDGGG SIIHIVDHLN LEAWSVPEVL RPLYESSKVV AQRMTIAALR YVRQIAQETS  420
GEVVYGLGRQ PAVLRTFSQR LSRGFNDAVN GFNDDGWSLM TCDGAEDVII AVNSTKSLST  480
TSNPTNSLAF LGGILCAKAS MLLQNVPPAL LVRFLREHRS EWADFNVDAY SAASLKAGSY  540
AYPGMRPTRF TGSQIIMPLG HTIEHEELLE VIRLEGHSLA QEDAFVSRDI HLLQICSGVD  600
ENAVGACSEL VFAPIDEMFP DDGPLLPSGF RIIPLDSKTP DTPDTLTAHR TLDLTSSLEV  660
GPATNPAAGD SSSCHHTRSV LTIAFQFPFE SNLQDNVATM ARQYVRSVIS SVQRVAMAIC  720
PSGLSPTLGP KLSPGSPEAL TLAHWICQSY SYHLGAELLR SDSVGGDSVL KNLWQHSDAI  780
LCCSLKSMPV FIFANQAGLD MLETTLVALQ DITLDKIFDE SGRKALCADF AKLMQQGFTY  840
LPAGICMSTM GRHVSYEQAV AWKVLAPEDN TVHCLAFSFI NWSFV*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ccl.205671e-125abscission zone
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}.
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_024034672.10.0homeobox-leucine zipper protein REVOLUTA isoform X1
SwissprotQ9SE430.0REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBLV4SG610.0V4SG61_9ROSI; Uncharacterized protein
STRINGXP_006424565.10.0(Citrus clementina)
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]