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 GRMZM2G056600_P01
Common Namecl52289_1b
Organism
Zea mays
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
Family HD-ZIP
Protein Properties Length: 261aa    MW: 28461.5 Da    PI: 4.5039
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM2G056600_P01genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.52.7e-1948101356
                        --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
           Homeobox   3 kRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                        k++++++eq+++Le+ Fe ++++  e++++LA+ lgL+ rqV vWFqNrRa++k
  GRMZM2G056600_P01  48 KKRRLSSEQVRALERSFEVENKLEPERKARLARDLGLQPRQVAVWFQNRRARWK 101
                        45689************************************************9 PP
2HD-ZIP_I/II134.43.9e-4347139193
        HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreelk 92 
                        ekkrrls+eqv++LE+sFe e+kLeperK++lar+LglqprqvavWFqnrRAR+ktkqlE+dy+aL+++ydal++++++L++++++L +e+k
  GRMZM2G056600_P01  47 EKKRRLSSEQVRALERSFEVENKLEPERKARLARDLGLQPRQVAVWFQNRRARWKTKQLERDYSALRQSYDALRHDHDALRRDKDALLAEIK 138
                        69**************************************************************************************9998 PP

        HD-ZIP_I/II  93 e 93 
                        e
  GRMZM2G056600_P01 139 E 139
                        7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466894.6E-2036105IPR009057Homeodomain-like
PROSITE profilePS5007117.57243103IPR001356Homeobox domain
SMARTSM003891.0E-1846107IPR001356Homeobox domain
CDDcd000867.48E-1948104No hitNo description
PfamPF000461.1E-1648101IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.4E-2049110IPR009057Homeodomain-like
PRINTSPR000318.6E-67483IPR000047Helix-turn-helix motif
PROSITE patternPS00027078101IPR017970Homeobox, conserved site
PRINTSPR000318.6E-68399IPR000047Helix-turn-helix motif
PfamPF021832.2E-17103144IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009637Biological Processresponse to blue light
GO:0030308Biological Processnegative regulation of cell growth
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0048573Biological Processphotoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0006310anatomytassel floret
PO:0006339anatomyjuvenile vascular leaf
PO:0006340anatomyadult vascular leaf
PO:0006341anatomyprimary shoot system
PO:0006354anatomyear floret
PO:0006505anatomycentral spike of ear inflorescence
PO:0008018anatomytransition vascular leaf
PO:0009001anatomyfruit
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009054anatomyinflorescence bract
PO:0009066anatomyanther
PO:0009074anatomystyle
PO:0009084anatomypericarp
PO:0009089anatomyendosperm
PO:0020040anatomyleaf base
PO:0020104anatomyleaf sheath
PO:0020126anatomytassel inflorescence
PO:0020127anatomyprimary root
PO:0020136anatomyear inflorescence
PO:0020142anatomystem internode
PO:0020148anatomyshoot apical meristem
PO:0025142anatomyleaf tip
PO:0025287anatomyseedling coleoptile
PO:0001007developmental stagepollen development stage
PO:0001009developmental stageD pollen mother cell meiosis stage
PO:0001052developmental stagevascular leaf expansion stage
PO:0001053developmental stagevascular leaf post-expansion stage
PO:0001083developmental stageinflorescence development stage
PO:0001094developmental stageplant embryo coleoptilar stage
PO:0001095developmental stageplant embryo true leaf formation stage
PO:0001180developmental stageplant proembryo stage
PO:0007001developmental stageearly whole plant fruit ripening stage
PO:0007003developmental stageIL.03 full inflorescence length reached stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
PO:0007015developmental stageradicle emergence stage
PO:0007016developmental stagewhole plant flowering stage
PO:0007022developmental stageseed imbibition stage
PO:0007026developmental stageFL.00 first flower(s) open stage
PO:0007031developmental stagemid whole plant fruit ripening stage
PO:0007032developmental stagewhole plant fruit formation stage up to 10%
PO:0007045developmental stagecoleoptile emergence stage
PO:0007063developmental stageLP.07 seven leaves visible stage
PO:0007065developmental stageLP.05 five leaves visible stage
PO:0007072developmental stageLP.18 eighteen leaves visible stage
PO:0007094developmental stageLP.01 one leaf visible stage
PO:0007101developmental stageLP.09 nine leaves visible stage
PO:0007104developmental stageLP.15 fifteen leaves visible stage
PO:0007106developmental stageLP.03 three leaves visible stage
PO:0007112developmental stage1 main shoot growth stage
PO:0007116developmental stageLP.11 eleven leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007633developmental stageendosperm development stage
PO:0021004developmental stageinflorescence initiation stage
Sequence ? help Back to Top
Protein Sequence    Length: 261 aa     Download sequence    Send to blast
MKRPRGASPP LAAMTNPNDD GYGVVGMEAD ADADADEEMM ACGGGGEKKR RLSSEQVRAL  60
ERSFEVENKL EPERKARLAR DLGLQPRQVA VWFQNRRARW KTKQLERDYS ALRQSYDALR  120
HDHDALRRDK DALLAEIKEL KAKLGDEEAA ASFTSVKAEP AASDGPPPVG VGSSESDSSA  180
VLNDADPPVA EAPVPEVRGT LLDAPGAVAA NHGGVFFHGS FLKVEEDETG LLDDDEPCGG  240
FFSVEQPPPM AWWTEPTEHW N
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
17278ERKARLA
295103RRARWKTKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Zm.45110.0ear| endosperm| meristem| ovary| shoot| tassel
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasGRMZM2G056600
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaf and floral organ primordia, floral meristems, embryonic axis and cells surrounding the vascular bundles. Expressed in the vasculature of roots, stem, leaves and spikelets, and in the vascular bundle of the scutellum in embryos. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
UniprotTISSUE SPECIFICITY: Expressed in leaf and floral organ primordia, floral meristems, embryonic axis and cells surrounding the vascular bundles. Expressed in the vasculature of roots, stem, leaves and spikelets, and in the vascular bundle of the scutellum in embryos. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'. May be involved in the regulation of gibberellin signaling. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:18049796}.
UniProtProbable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'. May be involved in the regulation of gibberellin signaling. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:18049796}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00051PBMTransfer from AT4G40060Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapGRMZM2G056600_P01
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By gibberellin. Down-regulated in leaves by drought stress. {ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
UniProtINDUCTION: By gibberellin. Down-regulated in leaves by drought stress. {ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0342570.0BT034257.1 Zea mays full-length cDNA clone ZM_BFc0009H14 mRNA, complete cds.
GenBankBT0390620.0BT039062.1 Zea mays full-length cDNA clone ZM_BFb0367N11 mRNA, complete cds.
GenBankBT0553740.0BT055374.1 Zea mays full-length cDNA clone ZM_BFb0091J03 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001140555.10.0uncharacterized protein LOC100272620
SwissprotQ6K4981e-126HOX4_ORYSJ; Homeobox-leucine zipper protein HOX4
SwissprotQ9XH371e-126HOX4_ORYSI; Homeobox-leucine zipper protein HOX4
TrEMBLB4FAW90.0B4FAW9_MAIZE; Homeobox-leucine zipper protein ATHB-6
TrEMBLK4JC730.0K4JC73_MAIZE; HB-type transcription factor (Fragment)
STRINGGRMZM2G056600_P010.0(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP30093482
Representative plantOGRP12916189
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G40060.12e-44homeobox protein 16
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]