PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G02560.2
Common NameLD, T10P11.15
Organism
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 HB-other
Protein Properties Length: 953aa    MW: 105415 Da    PI: 9.1457
Description HB-other family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G02560.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox18.14.7e-0666122157
                  TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS
     Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 
                  +r+R  ++++ ++ L+++F+ +  +s++e +e+++  g+t +qV+ +F  ++++ +k
  AT4G02560.2  66 KRPRDLLNPKAVKYLQAVFAIKDAISKRESREISALFGITVAQVREFFVTQKTRVRK 122
                  799*********************************************999999886 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS500719.57263123IPR001356Homeobox domain
SMARTSM003895.9E-565127IPR001356Homeobox domain
CDDcd000866.55E-466123No hitNo description
Gene3DG3DSA:1.10.10.607.5E-566125IPR009057Homeodomain-like
SuperFamilySSF466896.84E-666129IPR009057Homeodomain-like
Gene3DG3DSA:1.20.930.106.1E-5228323IPR017923Transcription factor IIS, N-terminal
SuperFamilySSF476761.18E-5231324IPR017923Transcription factor IIS, N-terminal
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009911Biological Processpositive regulation of flower development
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0030154Biological Processcell differentiation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
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:0025195anatomypollen tube cell
PO:0025281anatomypollen
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
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: 953 aa     Download sequence    Send to blast
MDAFKEEIEI GSSVESLMEL LDSQKVLFHS QIDQLQDVVV AQCKLTGVNP LAQEMAAGAL  60
SIKIGKRPRD LLNPKAVKYL QAVFAIKDAI SKRESREISA LFGITVAQVR EFFVTQKTRV  120
RKQVRLSREK VVMSNTHALQ DDGVPENNNA TNHVEPVPLN SIHPEACSIS WGEGETVALI  180
PPEDIPPDIS DSDKYFVENI FSLLRKEETF SGQVKLMEWI MQIQDASVLI WFLSKGGVLI  240
LTTWLSQAAS EEQTSVLLLI LKVLCHLPLH KASPENMSAI LQSVNGLRFY RISDISNRAK  300
GLLSRWTKLF AKIQAMKKQN RNSSQIDSQS QLLLKQSIAE IMGDSSNPED ILSLSNGKSE  360
NVRRIESSQG PKLLLTSADD STKKHMLGSN PSYNKERRKV QMVEQPGQKA AGKSPQTVRI  420
GTSGRSRPMS ADDIQKAKMR ALYMQSKNSK KDPLPSAIGD SKIVAPEKPL ALHSAKDSPP  480
IQNNEAKTED TPVLSTVQPV NGFSTIQPVN GPSAVQPVNG PLAVQPVNGP SALQPVNGPS  540
AVIVPVQADE IKKPSTPPKS ISSKVGVMMK MSSQTILKNC KRKQIDWHVP PGMELDELWR  600
VAAGGNSKEA DVQRNRNRRE RETTYQSLQT IPLNPKEPWD REMDYDDSLT PEIPSQQPPE  660
ESLTEPQDSL DERRIAAGAA TTSSSLSSPE PDLELLAALL KNPDLVYALT SGKPSNLAGQ  720
DMVKLLDVIK TGAPNSSSSS NKQVEERVEV SLPSPTPSTN PGMSGWGQEG IRNPFSRQNQ  780
VGTAVARSGT QLRVGSMQWH QTNEQSIPRH APSAYSNSIT LAHTEREQQQ YMQPKLHHNL  840
HFQQQQQQPI STTSYAVREP VGQMGTGTSS SWRSQQSQNS YYSHQENEIA SASQVTSYQG  900
NSQYMSSNPG YESWSPDNSP SRNQLNMRGQ QQQASRKHDS STHPYWNQNK RWR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.2400.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453399320.0
Genevisible255444_at0.0
Expression AtlasAT4G02560-
AtGenExpressAT4G02560-
ATTED-IIAT4G02560-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Accumulates prior to flowering in the vegetative shoot apical meristem and after flowering in floral meristems.
UniprotTISSUE SPECIFICITY: Expressed in shoot apex, root apex, leaf primordia and floral buds.
Functional Description ? help Back to Top
Source Description
TAIREncodes a nuclear localized protein with similarity to transcriptional regulators. Recessive mutants are late flowering. Expression of LFY is reduced in LD mutants.
UniProtSeems to play a role in the regulation of flowering time in the autonomous flowering pathway by repressing FLOWERING LOCUS C expression. {ECO:0000269|PubMed:10363371}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G02560.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G01530 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G45660(A), AT5G10140(R), AT5G61850(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G30970
IntActSearch Q38796
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Plants show late flowering phenotype (mutants LD-1 and LD-3). {ECO:0000269|PubMed:7907507}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G02560
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2267460.0AK226746.1 Arabidopsis thaliana mRNA for luminidependens protein, complete cds, clone: RAFL07-75-C15.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001190660.10.0homeobox protein LUMINIDEPENDENS
RefseqNP_192165.10.0homeobox protein LUMINIDEPENDENS
SwissprotQ387960.0LUMI_ARATH; Homeobox protein LUMINIDEPENDENS
TrEMBLD7M3G50.0D7M3G5_ARALL; Putative uncharacterized protein
STRINGAT4G02560.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Michaels SD,Amasino RM
    FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering.
    Plant Cell, 1999. 11(5): p. 949-56
    [PMID:10330478]
  2. Aukerman MJ,Lee I,Weigel D,Amasino RM
    The Arabidopsis flowering-time gene LUMINIDEPENDENS is expressed primarily in regions of cell proliferation and encodes a nuclear protein that regulates LEAFY expression.
    Plant J., 1999. 18(2): p. 195-203
    [PMID:10363371]
  3. Chou ML,Yang CH
    Late-flowering genes interact with early-flowering genes to regulate flowering time in Arabidopsis thaliana.
    Plant Cell Physiol., 1999. 40(7): p. 702-8
    [PMID:10501030]
  4. Soppe WJ,Bentsink L,Koornneef M
    The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana.
    Development, 1999. 126(21): p. 4763-70
    [PMID:10518493]
  5. Lee H, et al.
    The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis.
    Genes Dev., 2000. 14(18): p. 2366-76
    [PMID:10995392]
  6. van Nocke S,Muszynski M,Briggs K,Amasino RM
    Characterization of a gene from Zea mays related to the Arabidopsis flowering-time gene LUMINIDEPENDENS.
    Plant Mol. Biol., 2000. 44(1): p. 107-22
    [PMID:11094985]
  7. Michaels SD,Amasino RM
    Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization.
    Plant Cell, 2001. 13(4): p. 935-41
    [PMID:11283346]
  8. Schomburg FM,Patton DA,Meinke DW,Amasino RM
    FPA, a gene involved in floral induction in Arabidopsis, encodes a protein containing RNA-recognition motifs.
    Plant Cell, 2001. 13(6): p. 1427-36
    [PMID:11402170]
  9. Zhang H,van Nocker S
    The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C.
    Plant J., 2002. 31(5): p. 663-73
    [PMID:12207655]
  10. Noh YS,Amasino RM
    PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis.
    Plant Cell, 2003. 15(7): p. 1671-82
    [PMID:12837955]
  11. Tzeng TY,Hsiao CC,Chi PJ,Yang CH
    Two lily SEPALLATA-like genes cause different effects on floral formation and floral transition in Arabidopsis.
    Plant Physiol., 2003. 133(3): p. 1091-101
    [PMID:14526112]
  12. Boss PK,Bastow RM,Mylne JS,Dean C
    Multiple pathways in the decision to flower: enabling, promoting, and resetting.
    Plant Cell, 2004. 16 Suppl: p. S18-31
    [PMID:15037730]
  13. Lewandowska D, et al.
    Determinants of plant U12-dependent intron splicing efficiency.
    Plant Cell, 2004. 16(5): p. 1340-52
    [PMID:15100401]
  14. Nakagawa M,Komeda Y
    Flowering of Arabidopsis cop1 mutants in darkness.
    Plant Cell Physiol., 2004. 45(4): p. 398-406
    [PMID:15111714]
  15. Doyle MR, et al.
    HUA2 is required for the expression of floral repressors in Arabidopsis thaliana.
    Plant J., 2005. 41(3): p. 376-85
    [PMID:15659097]
  16. Werner JD, et al.
    FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions.
    Genetics, 2005. 170(3): p. 1197-207
    [PMID:15911588]
  17. Salathia N, et al.
    FLOWERING LOCUS C-dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways.
    BMC Plant Biol., 2006. 6: p. 10
    [PMID:16737527]
  18. Yoo SK,Lee JS,Ahn JH
    Overexpression of AGAMOUS-LIKE 28 (AGL28) promotes flowering by upregulating expression of floral promoters within the autonomous pathway.
    Biochem. Biophys. Res. Commun., 2006. 348(3): p. 929-36
    [PMID:16899218]
  19. Kim S,Choi K,Park C,Hwang HJ,Lee I
    SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger protein, represses flowering by transcriptional activation of Arabidopsis FLOWERING LOCUS C.
    Plant Cell, 2006. 18(11): p. 2985-98
    [PMID:17138694]
  20. Domagalska MA, et al.
    Attenuation of brassinosteroid signaling enhances FLC expression and delays flowering.
    Development, 2007. 134(15): p. 2841-50
    [PMID:17611230]
  21. Jin JB, et al.
    The SUMO E3 ligase, AtSIZ1, regulates flowering by controlling a salicylic acid-mediated floral promotion pathway and through affects on FLC chromatin structure.
    Plant J., 2008. 53(3): p. 530-40
    [PMID:18069938]
  22. Manzano C,Abraham Z,L
    Identification of ubiquitinated proteins in Arabidopsis.
    Plant Mol. Biol., 2008. 68(1-2): p. 145-58
    [PMID:18535787]
  23. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
    [PMID:18775970]
  24. Chang IF, et al.
    Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana.
    Proteomics, 2009. 9(11): p. 2967-85
    [PMID:19452453]
  25. Doyle MR,Amasino RM
    A single amino acid change in the enhancer of zeste ortholog CURLY LEAF results in vernalization-independent, rapid flowering in Arabidopsis.
    Plant Physiol., 2009. 151(3): p. 1688-97
    [PMID:19755537]
  26. Nah G,Jeffrey Chen Z
    Tandem duplication of the FLC locus and the origin of a new gene in Arabidopsis related species and their functional implications in allopolyploids.
    New Phytol., 2010. 186(1): p. 228-38
    [PMID:20100201]
  27. Tamura K,Fukao Y,Iwamoto M,Haraguchi T,Hara-Nishimura I
    Identification and characterization of nuclear pore complex components in Arabidopsis thaliana.
    Plant Cell, 2010. 22(12): p. 4084-97
    [PMID:21189294]
  28. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  29. Lee I, et al.
    Isolation of LUMINIDEPENDENS: a gene involved in the control of flowering time in Arabidopsis.
    Plant Cell, 1994. 6(1): p. 75-83
    [PMID:7907507]
  30. Sanda SL,Amasino RM
    Interaction of FLC and late-flowering mutations in Arabidopsis thaliana.
    Mol. Gen. Genet., 1996. 251(1): p. 69-74
    [PMID:8628249]
  31. Haung MD,Yang CH
    EMF genes interact with late-flowering genes to regulate Arabidopsis shoot development.
    Plant Cell Physiol., 1998. 39(4): p. 382-93
    [PMID:9615462]