PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G58780.3
Common NameAGL1, SHP1
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 MIKC_MADS
Protein Properties Length: 273aa    MW: 31481.8 Da    PI: 10.0497
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G58780.3genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF97.45.9e-312473150
                 S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
       SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                 krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva++ifs++g+lyey+
  AT3G58780.3 24 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALVIFSTRGRLYEYA 73
                 79***********************************************8 PP

2K-box116.23e-381202137100
        K-box   7 ksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100
                   s++ea+++++qqe++kL+++i+ +q+++Rh++Ge+L+sL++keL++Le +Lek+++++RskKnell+++ie++qk+e elq++n++Lr+k++e
  AT3G58780.3 120 PSVTEANTQYYQQEASKLRRQIRDIQNSNRHIVGESLGSLNFKELKNLEGRLEKGISRVRSKKNELLVAEIEYMQKREMELQHNNMYLRAKIAE 213
                  45899**************************************************************************************986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.3E-391675IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.3751676IPR002100Transcription factor, MADS-box
CDDcd002658.80E-391777No hitNo description
SuperFamilySSF554551.02E-291788IPR002100Transcription factor, MADS-box
PROSITE patternPS0035001872IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-321838IPR002100Transcription factor, MADS-box
PfamPF003193.9E-262572IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-323853IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-325374IPR002100Transcription factor, MADS-box
PfamPF014861.1E-27125211IPR002487Transcription factor, K-box
PROSITE profilePS5129715.162127217IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000019anatomygynoecium primordium
PO:0000035anatomycotyledon vascular system
PO:0000036anatomyleaf vascular system
PO:0000039anatomyshoot axis vascular system
PO:0000054anatomypetal vascular system
PO:0000056anatomyflower bud
PO:0000112anatomyshoot axis epidermis
PO:0000230anatomyinflorescence meristem
PO:0003011anatomyroot vascular system
PO:0004707anatomyfruit dehiscence zone
PO:0005645anatomyleaf mesophyll
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0009053anatomypeduncle
PO:0009067anatomyfilament
PO:0020003anatomyplant ovule
PO:0020139anatomyleaf midvein
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
PO:0007619developmental stageovule development stage
Sequence ? help Back to Top
Protein Sequence    Length: 273 aa     Download sequence    Send to blast
MEEGGSSHDA ESSKKLGRGK IEIKRIENTT NRQVTFCKRR NGLLKKAYEL SVLCDAEVAL  60
VIFSTRGRLY EYANNSFIYL LLEKKKKKKK KKNLWIYSSH VVRGTIERYK KACSDAVNPP  120
SVTEANTQYY QQEASKLRRQ IRDIQNSNRH IVGESLGSLN FKELKNLEGR LEKGISRVRS  180
KKNELLVAEI EYMQKREMEL QHNNMYLRAK IAEGARLNPD QQESSVIQGT TVYESGVSSH  240
DQSQHYNRNY IPVNLLEPNQ QFSGQDQPPL QLV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P6e-201683168Myocyte-specific enhancer factor 2B
1tqe_Q6e-201683168Myocyte-specific enhancer factor 2B
1tqe_R6e-201683168Myocyte-specific enhancer factor 2B
1tqe_S6e-201683168Myocyte-specific enhancer factor 2B
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
18391KKKKKKKKK
28591KKKKKKK
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible251555_at0.0
Expression AtlasAT3G58780-
AtGenExpressAT3G58780-
ATTED-IIAT3G58780-
Functional Description ? help Back to Top
Source Description
TAIROne of two genes (SHP1 and SHP2) that are required for fruit dehiscence. The two genes control dehiscence zone differentiation and promote the lignification of adjacent cells.
Function -- GeneRIF ? help Back to Top
  1. These experiments indicate that the ectopic co-expression of SEPALLATA3 and SHATTERPROOF1 and/or SEEDSTICK is probably not sufficient to homeotically transform vegetative tissues into carpels with ovules.
    [PMID: 16515858]
  2. SHP1 showed a low expression ALL, Childhood samples
    [PMID: 19206008]
  3. SHP1/2 and TAGL1, while distinct in molecular function, regulate similar activities via their necessity for seed dispersal in Arabidopsis and tomato, respectively.
    [PMID: 19880793]
  4. The present work identifies a new function for SHP1 and SHP2 genes in promoting stigma, style and medial tissue development.
    [PMID: 19900437]
  5. The stk shp1 shp2 ant quadruple mutant ovule lacks integument development as in ant single mutant.
    [PMID: 20041269]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00093SELEX26531826Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G58780.3
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 AT2G46870 (A), AT4G09960 (A), AT4G36920 (R), AT5G02030 (R), AT5G60910 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT4G00120(A), AT5G67110(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G61120, AT4G18960, AT4G24540, AT4G37940, AT5G13790, AT5G15800, AT1G24260, AT1G48150
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G58780
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankATHAGL1A0.0M55550.1 Arabidopsis thaliana transcription factor (AGL1), complete cds.
GenBankAY0861960.0AY086196.1 Arabidopsis thaliana clone 22339 mRNA, complete sequence.
GenBankJQ9730910.0JQ973091.1 Arabidopsis thaliana Shatterproof (SHP1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001190130.10.0agamous-like MADS-box protein AGL1
SwissprotP293811e-180AGL1_ARATH; Agamous-like MADS-box protein AGL1
TrEMBLF4J7050.0F4J705_ARATH; Agamous-like MADS-box protein AGL1
STRINGAT3G58780.30.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM33412350
Representative plantOGRP1617761
Publications ? help Back to Top
  1. Liljegren SJ, et al.
    SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis.
    Nature, 2000. 404(6779): p. 766-70
    [PMID:10783890]
  2. Smyth D
    A reverse trend--MADS functions revealed.
    Trends Plant Sci., 2000. 5(8): p. 315-7
    [PMID:10908873]
  3. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  4. M
    The MADS-box gene DEFH28 from Antirrhinum is involved in the regulation of floral meristem identity and fruit development.
    Plant J., 2001. 28(2): p. 169-79
    [PMID:11722760]
  5. Rajani S,Sundaresan V
    The Arabidopsis myc/bHLH gene ALCATRAZ enables cell separation in fruit dehiscence.
    Curr. Biol., 2001. 11(24): p. 1914-22
    [PMID:11747817]
  6. Parenicov√° L, et al.
    Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world.
    Plant Cell, 2003. 15(7): p. 1538-51
    [PMID:12837945]
  7. Favaro R, et al.
    MADS-box protein complexes control carpel and ovule development in Arabidopsis.
    Plant Cell, 2003. 15(11): p. 2603-11
    [PMID:14555696]
  8. Bao X,Franks RG,Levin JZ,Liu Z
    Repression of AGAMOUS by BELLRINGER in floral and inflorescence meristems.
    Plant Cell, 2004. 16(6): p. 1478-89
    [PMID:15155890]
  9. Moore RC,Grant SR,Purugganan MD
    Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2005. 22(1): p. 91-103
    [PMID:15371526]
  10. Lee JY, et al.
    Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis.
    Plant Cell, 2005. 17(1): p. 25-36
    [PMID:15598802]
  11. de Folter S, et al.
    Comprehensive interaction map of the Arabidopsis MADS Box transcription factors.
    Plant Cell, 2005. 17(5): p. 1424-33
    [PMID:15805477]
  12. Kaufmann K,Anfang N,Saedler H,Theissen G
    Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B sister (ABS) protein.
    Mol. Genet. Genomics, 2005. 274(2): p. 103-18
    [PMID:16080001]
  13. Causier B, et al.
    Evolution in action: following function in duplicated floral homeotic genes.
    Curr. Biol., 2005. 15(16): p. 1508-12
    [PMID:16111944]
  14. Battaglia R,Brambilla V,Colombo L,Stuitje AR,Kater MM
    Functional analysis of MADS-box genes controlling ovule development in Arabidopsis using the ethanol-inducible alc gene-expression system.
    Mech. Dev., 2006. 123(4): p. 267-76
    [PMID:16515858]
  15. Ma H,Yanofsky MF,Meyerowitz EM
    AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes.
    Genes Dev., 1991. 5(3): p. 484-95
    [PMID:1672119]
  16. de Folter S, et al.
    A Bsister MADS-box gene involved in ovule and seed development in petunia and Arabidopsis.
    Plant J., 2006. 47(6): p. 934-46
    [PMID:16925602]
  17. Brambilla V, et al.
    Genetic and molecular interactions between BELL1 and MADS box factors support ovule development in Arabidopsis.
    Plant Cell, 2007. 19(8): p. 2544-56
    [PMID:17693535]
  18. Mitsuda N,Ohme-Takagi M
    NAC transcription factors NST1 and NST3 regulate pod shattering in a partially redundant manner by promoting secondary wall formation after the establishment of tissue identity.
    Plant J., 2008. 56(5): p. 768-78
    [PMID:18657234]
  19. Mummenhoff K,Polster A,M
    Lepidium as a model system for studying the evolution of fruit development in Brassicaceae.
    J. Exp. Bot., 2009. 60(5): p. 1503-13
    [PMID:19052256]
  20. Gauffin F, et al.
    Expression of PTEN and SHP1, investigated from tissue microarrays in pediatric acute lymphoblastic, leukemia.
    Pediatr Hematol Oncol, 2009. 26(1): p. 48-56
    [PMID:19206008]
  21. Alvarez JP,Goldshmidt A,Efroni I,Bowman JL,Eshed Y
    The NGATHA distal organ development genes are essential for style specification in Arabidopsis.
    Plant Cell, 2009. 21(5): p. 1373-93
    [PMID:19435933]
  22. Mitsuda N,Ohme-Takagi M
    Functional analysis of transcription factors in Arabidopsis.
    Plant Cell Physiol., 2009. 50(7): p. 1232-48
    [PMID:19478073]
  23. Vrebalov J, et al.
    Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1.
    Plant Cell, 2009. 21(10): p. 3041-62
    [PMID:19880793]
  24. Colombo M, et al.
    A new role for the SHATTERPROOF genes during Arabidopsis gynoecium development.
    Dev. Biol., 2010. 337(2): p. 294-302
    [PMID:19900437]
  25. Losa A,Colombo M,Brambilla V,Colombo L
    Genetic interaction between AINTEGUMENTA (ANT) and the ovule identity genes SEEDSTICK (STK), SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2).
    Sex. Plant Reprod., 2010. 23(2): p. 115-21
    [PMID:20041269]
  26. Padilla-Chac
    Heterologous expression of yeast Hxt2 in Arabidopsis thaliana alters sugar uptake, carbon metabolism and gene expression leading to glucose tolerance of germinating seedlings.
    Plant Mol. Biol., 2010. 72(6): p. 631-41
    [PMID:20101436]
  27. Irish VF
    The flowering of Arabidopsis flower development.
    Plant J., 2010. 61(6): p. 1014-28
    [PMID:20409275]
  28. Matias-Hernandez L, et al.
    VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis.
    Plant Cell, 2010. 22(6): p. 1702-15
    [PMID:20581305]
  29. Gim
    Functional analysis of the Arlequin mutant corroborates the essential role of the Arlequin/TAGL1 gene during reproductive development of tomato.
    PLoS ONE, 2010. 5(12): p. e14427
    [PMID:21203447]
  30. Gomez MD,Urbez C,Perez-Amador MA,Carbonell J
    Characterization of constricted fruit (ctf) mutant uncovers a role for AtMYB117/LOF1 in ovule and fruit development in Arabidopsis thaliana.
    PLoS ONE, 2011. 6(4): p. e18760
    [PMID:21533201]
  31. Nanni L, et al.
    Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.).
    Theor. Appl. Genet., 2011. 123(8): p. 1341-57
    [PMID:21830108]
  32. Smaczniak C, et al.
    Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(5): p. 1560-5
    [PMID:22238427]
  33. Severing EI, et al.
    Predicting the impact of alternative splicing on plant MADS domain protein function.
    PLoS ONE, 2012. 7(1): p. e30524
    [PMID:22295091]
  34. Kim DY,Scalf M,Smith LM,Vierstra RD
    Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis.
    Plant Cell, 2013. 25(5): p. 1523-40
    [PMID:23667124]
  35. 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]
  36. Huang H, et al.
    DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation.
    Plant Cell, 1996. 8(1): p. 81-94
    [PMID:8597661]
  37. Flanagan CA,Hu Y,Ma H
    Specific expression of the AGL1 MADS-box gene suggests regulatory functions in Arabidopsis gynoecium and ovule development.
    Plant J., 1996. 10(2): p. 343-53
    [PMID:8771788]