PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT3G58780.1

Common Name

AGL1, SHP1, T20N10_130

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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: 248aa MW: 28335.8 Da PI: 9.397

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G58780.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	97.6	5.1e-31	24	73	1	50
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50 krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva++ifs++g+lyey+ AT3G58780.1 24 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALVIFSTRGRLYEYA 73 79***********************************************8 PP
2	K-box	116.5	2.5e-38	95	188	7	100
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 AT3G58780.1 95 PSVTEANTQYYQQEASKLRRQIRDIQNSNRHIVGESLGSLNFKELKNLEGRLEKGISRVRSKKNELLVAEIEYMQKREMELQHNNMYLRAKIAE 188 45899**************************************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	1.3E-39	16	75	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	33.375	16	76	IPR002100	Transcription factor, MADS-box
CDD	cd00265	7.11E-44	17	90	No hit	No description
SuperFamily	SSF55455	1.96E-32	17	88	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	18	72	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.2E-32	18	38	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.3E-26	25	72	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.2E-32	38	53	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.2E-32	53	74	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	9.2E-28	100	186	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.162	102	192	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0048481	Biological Process	plant ovule development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000019	anatomy	gynoecium primordium
PO:0000035	anatomy	cotyledon vascular system
PO:0000036	anatomy	leaf vascular system
PO:0000039	anatomy	shoot axis vascular system
PO:0000054	anatomy	petal vascular system
PO:0000056	anatomy	flower bud
PO:0000112	anatomy	shoot axis epidermis
PO:0000230	anatomy	inflorescence meristem
PO:0003011	anatomy	root vascular system
PO:0004707	anatomy	fruit dehiscence zone
PO:0005645	anatomy	leaf mesophyll
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0009053	anatomy	peduncle
PO:0009067	anatomy	filament
PO:0020003	anatomy	plant ovule
PO:0020139	anatomy	leaf midvein
PO:0025022	anatomy	collective leaf structure
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage
PO:0007619	developmental stage	ovule development stage

Sequence ? help Back to Top
Protein Sequence Length: 248 aa Download sequence Send to blast
MEEGGSSHDA ESSKKLGRGK IEIKRIENTT NRQVTFCKRR NGLLKKAYEL SVLCDAEVAL 60 VIFSTRGRLY EYANNSVRGT IERYKKACSD AVNPPSVTEA NTQYYQQEAS KLRRQIRDIQ 120 NSNRHIVGES LGSLNFKELK NLEGRLEKGI SRVRSKKNEL LVAEIEYMQK REMELQHNNM 180 YLRAKIAEGA RLNPDQQESS VIQGTTVYES GVSSHDQSQH YNRNYIPVNL LEPNQQFSGQ 240 DQPPLQLV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
1tqe_Q	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
1tqe_R	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
1tqe_S	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
5f28_A	4e-20	16	84	1	69	MEF2C
5f28_B	4e-20	16	84	1	69	MEF2C
5f28_C	4e-20	16	84	1	69	MEF2C
5f28_D	4e-20	16	84	1	69	MEF2C
6c9l_A	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
6c9l_B	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
6c9l_C	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
6c9l_D	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
6c9l_E	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
6c9l_F	4e-20	16	84	1	69	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	251555_at	0.0
Expression Atlas	AT3G58780	-
AtGenExpress	AT3G58780	-
ATTED-II	AT3G58780	-

Functional Description ? help Back to Top
Source	Description
TAIR	One 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.
UniProt	Probable transcription factor. Interacts genetically with TT16/AGL32 in a partially antagonistic manner during flower development. Is essential for the coordination of cell divisions in ovule, seed coat development and endosperm formation (PubMed:27776173). {ECO:0000269\|PubMed:27776173}.

Function -- GeneRIF ? help Back to Top
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] SHP1 showed a low expression ALL, Childhood samples [PMID: 19206008] 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] The present work identifies a new function for SHP1 and SHP2 genes in promoting stigma, style and medial tissue development. [PMID: 19900437] The stk shp1 shp2 ant quadruple mutant ovule lacks integument development as in ant single mutant. [PMID: 20041269] LAT and phospholipase C-gamma dephosphorylation by SHP-1 inhibits natural killer cell cytototoxicity [PMID: 27221712] Study identified new roles for SHP1 and SHP2: they are required for synchronized ovule maturation and subsequent fertilization/seed maturation, seed mucilage production, and have an inhibitory effect which is antagonistic to the ABS function in controlling formative divisions and cell shape of the inner integument and seed coat layers. [PMID: 27776173]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00093	SELEX	26531826	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G58780.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

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
BioGRID	AT3G61120, AT4G18960, AT4G24540, AT4G37940, AT5G13790, AT5G15800, AT1G24260, AT1G48150
IntAct	Search P29381

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G58780

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	ATHAGL1A	0.0	M55550.1 Arabidopsis thaliana transcription factor (AGL1), complete cds.
GenBank	AY086196	0.0	AY086196.1 Arabidopsis thaliana clone 22339 mRNA, complete sequence.
GenBank	JQ973091	0.0	JQ973091.1 Arabidopsis thaliana Shatterproof (SHP1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001325710.1	0.0	K-box region and MADS-box transcription factor family protein
Refseq	NP_191437.1	0.0	K-box region and MADS-box transcription factor family protein
Swissprot	P29381	0.0	AGL1_ARATH; Agamous-like MADS-box protein AGL1
TrEMBL	A0A1I9LM27	0.0	A0A1I9LM27_ARATH; K-box region and MADS-box transcription factor family protein
TrEMBL	A0A384LNV3	0.0	A0A384LNV3_ARATH; SHP1
TrEMBL	Q5XXJ3	0.0	Q5XXJ3_ARATH; SHATTERPROOF1
STRING	fgenesh2_kg.5__2325__AT3G58780.1	1e-180	(Arabidopsis lyrata)

Link Out ? help Back to Top
Phytozome	AT3G58780.1
Entrez Gene	825047
iHOP	AT3G58780
wikigenes	AT3G58780

Publications ? help Back to Top
Liljegren SJ, et al. SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature, 2000. 404(6779): p. 766-70 [PMID:10783890] Smyth D A reverse trend--MADS functions revealed. Trends Plant Sci., 2000. 5(8): p. 315-7 [PMID:10908873] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] 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] 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] Parenicová 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] 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] 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] 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] 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] 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] 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] Causier B, et al. Evolution in action: following function in duplicated floral homeotic genes. Curr. Biol., 2005. 15(16): p. 1508-12 [PMID:16111944] 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] 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] 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] 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] 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] 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] 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] 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] Mitsuda N,Ohme-Takagi M Functional analysis of transcription factors in Arabidopsis. Plant Cell Physiol., 2009. 50(7): p. 1232-48 [PMID:19478073] 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] 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] 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] 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] Irish VF The flowering of Arabidopsis flower development. Plant J., 2010. 61(6): p. 1014-28 [PMID:20409275] 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] 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] 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] 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] 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] 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] 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] 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] Matalon O, et al. Dephosphorylation of the adaptor LAT and phospholipase C-γ by SHP-1 inhibits natural killer cell cytotoxicity. Sci Signal, 2016. 9(429): p. ra54 [PMID:27221712] Ehlers K, et al. The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana. PLoS ONE, 2016. 11(10): p. e0165075 [PMID:27776173] 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] 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]