PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Thecc1EG002030t1
Common NameTCM_002030
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma
Family FAR1
Protein Properties Length: 843aa    MW: 96549.3 Da    PI: 7.0827
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG002030t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR188.96.9e-2880166291
              FAR1   2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleHnHelap 91 
                       fY+eYAk++GF++++++s++sk+++e+++++f Cs++g + e++     ++r++++++t+Cka+++vk++ dgkw ++++++eHnHel p
  Thecc1EG002030t1  80 FYQEYAKSMGFTTSIKNSRRSKKSKEFIDAKFACSRYGVTPESDVG---SSRRSSVKKTDCKASMHVKRRPDGKWIIHEFVKEHNHELLP 166
                       9***************************************999877...889999********************************975 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031012.6E-2580166IPR004330FAR1 DNA binding domain
PfamPF105513.7E-28286379IPR018289MULE transposase domain
PROSITE profilePS5096610.237566602IPR007527Zinc finger, SWIM-type
PfamPF044343.9E-7574601IPR007527Zinc finger, SWIM-type
SMARTSM005752.3E-7577604IPR006564Zinc finger, PMZ-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
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: 843 aa     Download sequence    Send to blast
MIKVRENQNA ISNMVDCRDA VPCIDGVNEN MVDIVDEAAH GRDGAIVDSS KRAVIGFEGD  60
TDFEPRNGIE FESHEAAYAF YQEYAKSMGF TTSIKNSRRS KKSKEFIDAK FACSRYGVTP  120
ESDVGSSRRS SVKKTDCKAS MHVKRRPDGK WIIHEFVKEH NHELLPALAY HFRIYRNVKL  180
AEKNNIDILN AVSERTRKMY VEMSRQSGGY QNVSLLQNDI KDQFDKGRHL VVDEGDAQIM  240
LEYFKRIKKE NPDFFYAIDL NEEQRLRNLF WVDAKSRKDY ASFSDVVSFD TTYVKFNEKL  300
PFAPFVGVNH HFQSMLLGCA LLADETKPTL VWLMKTWLRA MGGQAPKVII TDQDKALKAA  360
VQEVFPTARH CFALWHILEK IPKSLAHVIG QHENFLPKFN KCIFKSWTDE GFDMRWWKMI  420
TRFELQDDEW VQSLYEDRKR WVPTFMDDVF LAGMSTSQRS ESMNSFFDKY IHKKITLKEF  480
VKQYGAILQN RYEEEAVADF DTWQKQPALK SPSPWEKQMS IVYTHAIFKK FQVEVLGVVG  540
CHPKRENEDE GTITFRVQDC EKDENFLVIW NEEKSEVSCS CHMFEYRGFL CRHAMIVLQM  600
CGRTSIPPCY ILKRWTKDAK SGQSTAEGTD RVQTRVQRYN ELCKQAIELS EEGSLSEESH  660
NIAFRALVEA LKNCVNVNNS CISAVESVGH AHGLRETVEE NQGSLASKSS KKKNTNKKRK  720
GQSEPALMFV DAQDSLQQME NLSSDGISLN GYYGAQQNVQ GLVQLNLMEP PHDGYYVNQQ  780
SMQGLGQLNS IAPSHDSFFG TQQSMHGLGQ LDYRPPASFS YALQDEPQLR STQLHGGVSR  840
HP*
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
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_007049034.20.0PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1
SwissprotQ9SWG30.0FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBLA0A061DMC60.0A0A061DMC6_THECC; FRS (FAR1 Related Sequences) transcription factor family
STRINGEOX931910.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM11826253
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. 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]
  2. 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]
  3. Motamayor JC, et al.
    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
    Genome Biol., 2013. 14(6): p. r53
    [PMID:23731509]
  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]