PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc08g060840.1.1
Common NameLOC101258392
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family FAR1
Protein Properties Length: 827aa    MW: 94634.5 Da    PI: 7.5858
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc08g060840.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR187.71.7e-2767152290
                FAR1   2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleHnHela 90 
                         fY+eYAk++GF++++++s++sk+++e+++++f Cs++g++ e+++    ++r+ ++++t+Cka+++vk+++dgkw+v+++ ++HnH l 
  Solyc08g060840.1.1  67 FYQEYAKSMGFTTSIKNSRRSKKSKEFIDAKFACSRYGTTPESDTG---SSRRPSVKKTDCKASMHVKRKRDGKWYVHEFIKDHNHGLL 152
                         9***************************************999877...77888899*****************************997 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031015.2E-2567153IPR004330FAR1 DNA binding domain
PfamPF105516.5E-25273365IPR018289MULE transposase domain
PROSITE profilePS5096610.039553589IPR007527Zinc finger, SWIM-type
PfamPF044348.1E-7563588IPR007527Zinc finger, SWIM-type
SMARTSM005751.2E-8564591IPR006564Zinc finger, PMZ-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009585Biological Processred, far-red light phototransduction
GO:0010018Biological Processfar-red light signaling pathway
GO:0042753Biological Processpositive regulation of circadian rhythm
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 827 aa     Download sequence    Send to blast
MVDHGDVVQS SVQLTGDMVD AVDKSCLSRD GGVSRSPKRS ITGVEEHADF EPHDGIEFES  60
HEAAYAFYQE YAKSMGFTTS IKNSRRSKKS KEFIDAKFAC SRYGTTPESD TGSSRRPSVK  120
KTDCKASMHV KRKRDGKWYV HEFIKDHNHG LLPALAYHFR IHRNVKLAEK NNIDILNAVS  180
ERTRKMYVEM SRQCGGSQEV GLLTNDLNYQ FDKGRCLSLE EGDAHIMLEY FMHVQKENPC  240
FFYATDLNED QRLRNLFWID AKSRKDYVSF NDVVFFDTSY MKSNEKMPFA LLIGVNHHCQ  300
PMLLGCALIA DETKPTFVWL MKTWLRAVGG KAPKVIIADQ DKSLKSALEE VFPCSSHCFA  360
LWHVLERIPE TLAHVVKQHE NFMQKFSKCI FKSLTDEQFD LRWWKMVSRF ELQENEWIHT  420
LYEDRKKWIP AYMRGSFMAG MSTAQRSESI SSFFDKYIHK KISLKEFMRQ YGMILQNRYE  480
EEAIADFDTL HKLPALKSPS PWEKQMSTIY THTIFKKFQV EVLGVVGCHP KKEAVNGENV  540
TFRVDDCEKD ENFMVTWNEA RSDVSCSCLL FEYNGFLCRH AMIVLQMCGL SIIPSQYILK  600
RWTKDAKNIQ LISEGTERIR NRVQRYNDLC RRAIELGVEG SLSEESYGVA FRALDEALKN  660
CVNVNNRSSA LTECSSSAVG LRDLEEDTQG IHAIKTSRKK NTNKKRKMHS EPEAAIVEAK  720
DSLQQMDSLT VGGMTLNGYY GTHQNVQGLI QLNLMEPPHD GYYVNQQNMQ GLGQLNTIAP  780
GHDGFFGSQQ SIPGLGHLDF RQPSFTYGLQ DEPSLRAAQL HGNNAR*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.84370.0callus| flower
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269|PubMed:11889039, ECO:0000269|PubMed:12753585, ECO:0000269|PubMed:18033885, ECO:0000269|PubMed:22634759}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00434DAPTransfer from AT4G15090Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc08g060840.1.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated after exposure to far-red light. Subject to a negative feedback regulation by PHYA signaling. {ECO:0000269|PubMed:18033885}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004245025.10.0protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
RefseqXP_010324981.10.0protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
RefseqXP_010324983.10.0protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
SwissprotQ9SWG30.0FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBLK4CKM90.0K4CKM9_SOLLC; Uncharacterized protein
STRINGSolyc08g060840.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49621103
Representative plantOGRP1345734
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G15090.10.0FAR1 family protein
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. Domergue F, et al.
    Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition.
    Plant Physiol., 2010. 153(4): p. 1539-54
    [PMID:20571114]
  3. Heyndrickx KS,Vandepoele K
    Systematic identification of functional plant modules through the integration of complementary data sources.
    Plant Physiol., 2012. 159(3): p. 884-901
    [PMID:22589469]
  4. Wang C, et al.
    SCAB3 Is Required for Reorganization of Actin Filaments during Light Quality Changes.
    J Genet Genomics, 2015. 42(4): p. 161-8
    [PMID:25953354]
  5. Wang W, et al.
    A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis.
    J Integr Plant Biol, 2016. 58(1): p. 91-103
    [PMID:25989254]
  6. Ma L, et al.
    Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1.
    Mol Plant, 2016. 9(4): p. 541-57
    [PMID:26714049]
  7. Siddiqui H,Khan S,Rhodes BM,Devlin PF
    FHY3 and FAR1 Act Downstream of Light Stable Phytochromes.
    Front Plant Sci, 2016. 7: p. 175
    [PMID:26941752]
  8. Liu L,Li B,Liu X
    FAR-RED ELONGATED HYPOCOTYL3 promotes floral meristem determinacy in Arabidopsis.
    Plant Signal Behav, 2016. 11(10): p. e1238545
    [PMID:27660915]
  9. Ma L,Xue N,Fu X,Zhang H,Li G
    Arabidopsis thaliana FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar.
    New Phytol., 2017. 213(4): p. 1682-1696
    [PMID:27859295]
  10. Liu Y, et al.
    Light and Ethylene Coordinately Regulate the Phosphate Starvation Response through Transcriptional Regulation of PHOSPHATE STARVATION RESPONSE1.
    Plant Cell, 2017. 29(9): p. 2269-2284
    [PMID:28842534]
  11. Joly-Lopez Z, et al.
    Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements.
    Front Plant Sci, 2017. 8: p. 2027
    [PMID:29250089]