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 AT5G48150.1
Common NameMIF21.4, PAT1
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family GRAS
Protein Properties Length: 490aa    MW: 55290.1 Da    PI: 6.584
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G48150.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS462.52.5e-1411204902374
         GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaN 99 
                  +  L++cA+a+s++dl +a++++++l++++s +g+p+qRl ay++e+L a+la+s+s++ykal+  +++   s+e l+++++++ev+P++kf+++ aN
  AT5G48150.1 120 RADLVSCAKAMSENDLMMAHSMMEKLRQMVSVSGEPIQRLGAYLLEGLVAQLASSGSSIYKALNRCPEP--ASTELLSYMHILYEVCPYFKFGYMSAN 215
                  678************************************************************666665..499************************ PP

         GRAS 100 qaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakfAeelgvpfefnvlvakrledleleeLr 195
                   aI ea+++e+rvHiiDf+i+qG QW++L+qa+a+Rp+gpp++RiTg+++++s   +   l+ +g+rLak+A++++vpfefn  v+ +++++++++L 
  AT5G48150.1 216 GAIAEAMKEENRVHIIDFQIGQGSQWVTLIQAFAARPGGPPRIRITGIDDMTSAyaRGGGLSIVGNRLAKLAKQFNVPFEFNS-VSVSVSEVKPKNLG 312
                  **************************************************999999999************************.7999********** PP

         GRAS 196 vkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgre 293
                  v+pgEalaVn+++ lh+++desvs+e++rd++L++vkslsPkvv++veqe+++n++ F+ rf+e+++yy+a+f+s++++lpr++++ri+vE+++l+r+
  AT5G48150.1 313 VRPGEALAVNFAFVLHHMPDESVSTENHRDRLLRMVKSLSPKVVTLVEQESNTNTAAFFPRFMETMNYYAAMFESIDVTLPRDHKQRINVEQHCLARD 410
                  ************************************************************************************************** PP

         GRAS 294 ivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                  +vn++acega+r+erhe l+kWr+r+++aGF+p+pls  +++++k+llr+++++ yr+ee++g+l+lgW++r Lv+ +aW+
  AT5G48150.1 411 VVNIIACEGADRVERHELLGKWRSRFGMAGFTPYPLSPLVNSTIKSLLRNYSDK-YRLEERDGALYLGWMHRDLVASCAWK 490
                  ****************************************************55.*************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098570.67393471IPR005202Transcription factor GRAS
PfamPF035148.6E-139120490IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007165Biological Processsignal transduction
GO:0009640Biological Processphotomorphogenesis
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0004871Molecular Functionsignal transducer activity
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 490 aa     Download sequence    Send to blast
MYKQPRQELE AYYFEPNSVE KLRYLPVNNS RKRFCTLEPF PDSPPYNALS TATYDDTCGS  60
CVTDELNDFK HKIREIETVM MGPDSLDLLV DCTDSFDSTA SQEINGWRST LEAISRRDLR  120
ADLVSCAKAM SENDLMMAHS MMEKLRQMVS VSGEPIQRLG AYLLEGLVAQ LASSGSSIYK  180
ALNRCPEPAS TELLSYMHIL YEVCPYFKFG YMSANGAIAE AMKEENRVHI IDFQIGQGSQ  240
WVTLIQAFAA RPGGPPRIRI TGIDDMTSAY ARGGGLSIVG NRLAKLAKQF NVPFEFNSVS  300
VSVSEVKPKN LGVRPGEALA VNFAFVLHHM PDESVSTENH RDRLLRMVKS LSPKVVTLVE  360
QESNTNTAAF FPRFMETMNY YAAMFESIDV TLPRDHKQRI NVEQHCLARD VVNIIACEGA  420
DRVERHELLG KWRSRFGMAG FTPYPLSPLV NSTIKSLLRN YSDKYRLEER DGALYLGWMH  480
RDLVASCAWK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A2e-661234908375GRAS family transcription factor containing protein, expressed
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.70760.0bud| flower| leaf| root
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible248689_at0.0
Expression AtlasAT5G48150-
AtGenExpressAT5G48150-
ATTED-IIAT5G48150-
Functional Description ? help Back to Top
Source Description
TAIRMember of GRAS gene family. Semi-dominant mutant has a reduced response to far-red light and appears to act early in the phytochrome A signaling pathway.
UniProtProbable transcription factor involved in phytochrome A (phyA) signal transduction. {ECO:0000269|PubMed:10817761}.
Function -- GeneRIF ? help Back to Top
  1. Both PAT1 and SCL21 are involved in phyA-dependent signaling.
    [PMID: 23109688]
  2. The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2.
    [PMID: 25603932]
  3. The heterodimeric transcription factor complex ETHYLENE RESPONSE FACTOR115 (ERF115)-PHYTOCHROME A SIGNAL TRANSDUCTION1 (PAT1) sustains meristem function by promoting cell renewal after stem cell loss.
    [PMID: 27797356]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G48150.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Plants display reduced response to far-red (FR) light. Seedlings develop long hypocotyls, unfolded cotyledons, no significant anthocyanin accumulation, and greening after FR light. {ECO:0000269|PubMed:10817761}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G48150
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1534430.0AF153443.1 Arabidopsis thaliana phytochrome A signal transduction 1 protein (PAT1) mRNA, complete cds.
GenBankAK3172520.0AK317252.1 Arabidopsis thaliana AT5G48150 mRNA, complete cds, clone: RAFL22-43-D17.
GenBankAK3177470.0AK317747.1 Arabidopsis thaliana AT5G48150 mRNA, complete cds, clone: RAFL22-04-F15.
GenBankBT0253260.0BT025326.1 Arabidopsis thaliana At5g48150 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001332482.10.0GRAS family transcription factor
RefseqNP_001332483.10.0GRAS family transcription factor
RefseqNP_199626.10.0GRAS family transcription factor
RefseqNP_974903.10.0GRAS family transcription factor
SwissprotQ9LDL70.0PAT1_ARATH; Scarecrow-like transcription factor PAT1
TrEMBLB9DGR40.0B9DGR4_ARATH; AT5G48150 protein
STRINGAT5G48150.20.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM62128141
Representative plantOGRP14091447
Publications ? help Back to Top
  1. Bolle C,Koncz C,Chua NH
    PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction.
    Genes Dev., 2000. 14(10): p. 1269-78
    [PMID:10817761]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
    [PMID:11910074]
  4. McCormac AC,Terry MJ
    Light-signalling pathways leading to the co-ordinated expression of HEMA1 and Lhcb during chloroplast development in Arabidopsis thaliana.
    Plant J., 2002. 32(4): p. 549-59
    [PMID:12445126]
  5. Tian C,Wan P,Sun S,Li J,Chen M
    Genome-wide analysis of the GRAS gene family in rice and Arabidopsis.
    Plant Mol. Biol., 2004. 54(4): p. 519-32
    [PMID:15316287]
  6. Brenner WG,Romanov GA,K
    Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades.
    Plant J., 2005. 44(2): p. 314-33
    [PMID:16212609]
  7. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  8. Torres-Galea P,Huang LF,Chua NH,Bolle C
    The GRAS protein SCL13 is a positive regulator of phytochrome-dependent red light signaling, but can also modulate phytochrome A responses.
    Mol. Genet. Genomics, 2006. 276(1): p. 13-30
    [PMID:16680434]
  9. Lee MH, et al.
    Large-scale analysis of the GRAS gene family in Arabidopsis thaliana.
    Plant Mol. Biol., 2008. 67(6): p. 659-70
    [PMID:18500650]
  10. Klopffleisch K, et al.
    Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.
    Mol. Syst. Biol., 2011. 7: p. 532
    [PMID:21952135]
  11. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
    [PMID:22995285]
  12. Torres-Galea P,Hirtreiter B,Bolle C
    Two GRAS proteins, SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1, function cooperatively in phytochrome A signal transduction.
    Plant Physiol., 2013. 161(1): p. 291-304
    [PMID:23109688]
  13. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  14. Roux ME, et al.
    The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2.
    EMBO J., 2015. 34(5): p. 593-608
    [PMID:25603932]
  15. Heyman J, et al.
    The heterodimeric transcription factor complex ERF115-PAT1 grants regeneration competence.
    Nat Plants, 2016. 2(11): p. 16165
    [PMID:27797356]