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

AT5G60440.1

Common Name

AGL62, MUF9.24

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

M-type_MADS

Protein Properties

Length: 299aa MW: 34587.8 Da PI: 9.1805

Description

AGAMOUS-like 62

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G60440.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	69.9	2.4e-22	16	62	3	49
--SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEE CS SRF-TF 3 ienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyey 49 +n+sn qvtfskRr g++KKA+EL++LC+aeva+++fs+ k++ + AT5G60440.1 16 MKNESNLQVTFSKRRSGLFKKASELCTLCGAEVAIVVFSPGRKVFSF 62 589*************************************9999877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	24.32	6	66	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.8E-31	6	65	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	5.49E-28	7	86	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.69E-33	7	78	No hit	No description
PRINTS	PR00404	1.3E-18	8	28	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.7E-24	16	62	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-18	28	43	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-18	43	64	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009960	Biological Process	endosperm development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0009005	anatomy	root
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009089	anatomy	endosperm
PO:0020093	anatomy	antipodal cell
PO:0020100	anatomy	hypocotyl
PO:0025022	anatomy	collective leaf structure
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 299 aa Download sequence Send to blast
MVKKSKGRQK IEMVKMKNES NLQVTFSKRR SGLFKKASEL CTLCGAEVAI VVFSPGRKVF 60 SFGHPNVDSV IDRFINNNPL PPHQHNNMQL RETRRNSIVQ DLNNHLTQVL SQLETEKKKY 120 DELKKIREKT KALGNWWEDP VEELALSQLE GFKGNLENLK KVVTVEASRF FQANVPNFYV 180 GSSSNNAAFG IDDGSHINPD MDLFSQRRMM DINAFNYNQN QIHPNHALPP FGNNAYGINE 240 GFVPEYNVNF RPEYNPNQNQ IQNQNQVQIQ IQNQSFKREN ISEYEHHHGY PPQSRSDYY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1c7u_A	8e-15	7	84	1	76	MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, C4 FORM
1c7u_B	8e-15	7	84	1	76	MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, C4 FORM
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Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	240256463	0.0
Genevisible	247631_at	0.0
Expression Atlas	AT5G60440	-
AtGenExpress	AT5G60440	-
ATTED-II	AT5G60440	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed during the syncytial endosperm development. {ECO:0000269\|PubMed:18334668}.
Uniprot	TISSUE SPECIFICITY: Expressed in the endosperm but not in the embryo. Detected in young siliques, roots, leaves, stems, young flowers and anthers. {ECO:0000269\|PubMed:18334668}.

Functional Description ? help Back to Top
Source	Description
TAIR	AGL62 encodes a Type I MADS domain protein that likely functions as a transcription factor. It is expressed AGL62 is expressed exclusively in the endosperm. AGL62 supresses suppresses cellularization during the syncytial phase of endosperm development.
UniProt	Probable transcription factor. Required for suppression of cellularization and promotion of nuclear proliferation during early endosperm development. The FERTILIZATION-INDEPENDENT SEED (FIS) polycomb complex is required for suppression of ALG62 expression at the end of the syncytial phase of endosperm development. {ECO:0000269\|PubMed:18334668}.

Function -- GeneRIF ? help Back to Top
Data suggest that AGL62 suppresses cellularization during the syncytial phase of endosperm development and that endosperm cellularization is triggered via direct or indirect AGL62 inactivation by the FIS polycomb complex. [PMID: 18334668] AGL62 is a direct target gene of FIS Polycomb group repressive complex 2 (PRC2), establishing the molecular basis for FIS PRC2-mediated endosperm cellularization. [PMID: 22535409]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G60440.1

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

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G31630, AT1G31640, AT1G46408, AT1G65300, AT1G65330
IntAct	Search Q9FKK2

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G60440

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EU493093	0.0	EU493093.1 Arabidopsis thaliana MADS-box protein AGL62 (AGL62) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_200852.1	0.0	AGAMOUS-like 62
Swissprot	Q9FKK2	0.0	AGL62_ARATH; Agamous-like MADS-box protein AGL62
TrEMBL	A0A178UGT8	0.0	A0A178UGT8_ARATH; AGL62
STRING	AT5G60440.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM86	28	390
Representative plant	OGRP16	17	761

Link Out ? help Back to Top
Phytozome	AT5G60440.1
Entrez Gene	836165
iHOP	AT5G60440
wikigenes	AT5G60440

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] De Bodt S, et al. Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J. Mol. Evol., 2003. 56(5): p. 573-86 [PMID:12698294] 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] Kofuji R, et al. Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses. Mol. Biol. Evol., 2003. 20(12): p. 1963-77 [PMID:12949148] 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] Pina C,Pinto F,Feij Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol., 2005. 138(2): p. 744-56 [PMID:15908605] Kang IH,Steffen JG,Portereiko MF,Lloyd A,Drews GN The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis. Plant Cell, 2008. 20(3): p. 635-47 [PMID:18334668] Bemer M,Wolters-Arts M,Grossniklaus U,Angenent GC The MADS domain protein DIANA acts together with AGAMOUS-LIKE80 to specify the central cell in Arabidopsis ovules. Plant Cell, 2008. 20(8): p. 2088-101 [PMID:18713950] Day RC,Herridge RP,Ambrose BA,Macknight RC Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. Plant Physiol., 2008. 148(4): p. 1964-84 [PMID:18923020] Walia H, et al. Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr. Biol., 2009. 19(13): p. 1128-32 [PMID:19559614] Bemer M,Heijmans K,Airoldi C,Davies B,Angenent GC An atlas of type I MADS box gene expression during female gametophyte and seed development in Arabidopsis. Plant Physiol., 2010. 154(1): p. 287-300 [PMID:20631316] Roszak P,K Polycomb group proteins are required to couple seed coat initiation to fertilization. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(51): p. 20826-31 [PMID:22143805] Hehenberger E,Kradolfer D,K Endosperm cellularization defines an important developmental transition for embryo development. Development, 2012. 139(11): p. 2031-9 [PMID:22535409] Ngo QA, et al. The Armadillo repeat gene ZAK IXIK promotes Arabidopsis early embryo and endosperm development through a distinctive gametophytic maternal effect. Plant Cell, 2012. 24(10): p. 4026-43 [PMID:23064319] Kradolfer D,Hennig L,K Increased maternal genome dosage bypasses the requirement of the FIS polycomb repressive complex 2 in Arabidopsis seed development. PLoS Genet., 2013. 9(1): p. e1003163 [PMID:23326241] Xu W, et al. Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds. Plant Cell, 2016. 28(6): p. 1343-60 [PMID:27233529] Figueiredo DD,Batista RA,Roszak PJ,Köhler C Auxin production couples endosperm development to fertilization. Nat Plants, 2015. 1: p. 15184 [PMID:27251719] Figueiredo DD,Batista RA,Roszak PJ,Hennig L,Köhler C Auxin production in the endosperm drives seed coat development in Arabidopsis. Elife, 2017. [PMID:27848912] Fiume E,Coen O,Xu W,Lepiniec L,Magnani E Growth of the Arabidopsis sub-epidermal integument cell layers might require an endosperm signal. Plant Signal Behav, 2017. 12(8): p. e1339000 [PMID:28613109] Zhang S, et al. FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development. Plant Physiol., 2018. 177(1): p. 285-299 [PMID:29523711]