PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Gorai.003G142200.1
Common NameB456_003G142200, LOC105788948
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family HD-ZIP
Protein Properties Length: 846aa    MW: 92554.3 Da    PI: 5.8869
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.003G142200.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox57.42.5e-182785357
                        --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
            Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                        k  ++t+eq+e+Le++++++++ps  +r++L +++    +++ +q+kvWFqNrR +ek+
  Gorai.003G142200.1 27 KYVRYTAEQVEALERVYAECPKPSSLRRQQLIRECpilsNIEPKQIKVWFQNRRCREKQ 85
                        56789****************************************************97 PP
2START159.82.1e-501663742205
                         HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EE CS
               START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..ga 90 
                         +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+++sg a+ra+g+v  +++   +e+l+d++ W ++++  e+      g  g+
  Gorai.003G142200.1 166 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQSCSGVAARACGLVSLEPT-KIAEILKDRPSWLRDCRNLEVFTMFPAGsgGT 255
                         7899******************************************************.7777777777*******9999999999888** PP

                         EEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXX CS
               START  91 lqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlp 177
                         ++l ++++ a+++l+p Rdf+++Ry+ +l+ g++v++++S++     p+    +++vRae+lpSg+li+p+++g+s +++v+h +l+++++
  Gorai.003G142200.1 256 IELVYTQMFAPTTLAPaRDFWTLRYTTTLENGSFVVCERSLSGSGAGPStaaAAQFVRAEVLPSGYLIRPCEGGGSIIHIVDHLNLEAWSV 346
                         ******************************************88888877999************************************** PP

                         HHHHHHHHHHHHHHHHHHHHHHTXXXXX CS
               START 178 hwllrslvksglaegaktwvatlqrqce 205
                         +++lr+l++s+ + ++k++ a+l++ ++
  Gorai.003G142200.1 347 PEVLRPLYESSKVIAQKMTIAALRYVKQ 374
                         ***********************99876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007115.3372286IPR001356Homeobox domain
SuperFamilySSF466892.18E-162388IPR009057Homeodomain-like
SMARTSM003891.7E-152490IPR001356Homeobox domain
CDDcd000864.82E-162787No hitNo description
PfamPF000467.5E-162885IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.0E-182985IPR009057Homeodomain-like
CDDcd146864.89E-679118No hitNo description
PROSITE profilePS5084827.397156384IPR002913START domain
CDDcd088751.69E-68160376No hitNo description
SuperFamilySSF559611.25E-33165377No hitNo description
Gene3DG3DSA:3.30.530.201.2E-19165370IPR023393START-like domain
SMARTSM002347.8E-42165375IPR002913START domain
PfamPF018524.8E-48166374IPR002913START domain
SuperFamilySSF559616.59E-5406500No hitNo description
SuperFamilySSF559616.59E-5535599No hitNo description
PfamPF086703.8E-50701844IPR013978MEKHLA
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: 846 aa     Download sequence    Send to blast
MAMAVAQHRV STSGSSSINK HLDASGKYVR YTAEQVEALE RVYAECPKPS SLRRQQLIRE  60
CPILSNIEPK QIKVWFQNRR CREKQRKESS RLQTVNRKLS AMNKLLMEEN DRLQKQVSQL  120
VCENGYMRQQ LHTVNASATD ASCDSVVTTP QHSLRDPTNP AGLLSIAEET LAEFLSKATG  180
TAVDWVQMPG MKPGPDSVGI FAISQSCSGV AARACGLVSL EPTKIAEILK DRPSWLRDCR  240
NLEVFTMFPA GSGGTIELVY TQMFAPTTLA PARDFWTLRY TTTLENGSFV VCERSLSGSG  300
AGPSTAAAAQ FVRAEVLPSG YLIRPCEGGG SIIHIVDHLN LEAWSVPEVL RPLYESSKVI  360
AQKMTIAALR YVKQIAQETS GEVVYSMGRQ PAVLRTFSQR LSRGFNDAIN GFNDDGWSIM  420
NCDGNEDVII AINSSKSFSC TSNPNNALPF VGGVLCAKAS MLLQNVPPAV LVRFLREHRS  480
EWADFNVDAY TAASLKAGTY AYPGMRPTRF SGSQIIMPLG HTIEHEEILE VIRLEGHSLV  540
QEDAFVSRDI HLLQICSGID ENAVGACSEL VFAPIDEMFP DDAPLIPSGF RIIPLESKPA  600
DTQDSLTTNR TLDLTSSLEV GPATNHSSGD VPSSQNSRSV LTIAFQFPFD SSLQDNVATM  660
ARQYVRSVIS SVQRVATAIS PSGLSADVGP KLSPGSPEAL TLAQWICQSY SYHIGAELLR  720
SESLGSDSML KNLWQHQDAI LCCSLKSLPV FIFANQAGLD MLETTLVSLQ DITLDKIFDE  780
PGRKALCSDF AKLMQQGYAY FPAGICMSTM GRHVSYEQAV AWKVLEADES TVHCLAFSFV  840
NWSFV*
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_012471510.10.0PREDICTED: homeobox-leucine zipper protein REVOLUTA-like isoform X2
SwissprotQ9SE430.0REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBLA0A0D2MNN90.0A0A0D2MNN9_GOSRA; Uncharacterized protein
STRINGGorai.003G142200.10.0(Gossypium raimondii)
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. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  2. 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]
  3. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  4. 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]
  5. 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]
  6. 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]
  7. 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]