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

AT5G23260.2

Common Name

ABS, AGL32, MKD15.12, TT16

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: 252aa MW: 29697.5 Da PI: 6.5865

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G23260.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	77.4	1e-24	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 k+ien++ rqvtfskRr+g++KK ELS+LCda + +i+fs tgkl e++s AT5G23260.2 9 KKIENQTARQVTFSKRRTGLIKKTRELSILCDAHIGLIVFSATGKLSEFCS 59 68***********************************************96 PP
2	K-box	59.7	1.2e-20	83	168	11	96
K-box 11 eakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 + ++e+l++e++ L++e+ nL+ +R + G dL s+ +eL Le+qLe+s+ k+R++Knel+ +q+e+l +k ++l+e+n+++ + AT5G23260.2 83 HDDQEQLHHEMELLRRETCNLELRLRPFHGHDLASIPPNELDGLERQLEHSVLKVRERKNELMQQQLENLSRKRRMLEEDNNNMYR 168 566899***************************************************************************99866 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	29.955	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	9.8E-38	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	3.79E-31	2	92	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.81E-42	2	79	No hit	No description
PRINTS	PR00404	2.7E-26	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.6E-23	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.7E-26	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.7E-26	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	1.1E-19	82	170	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	14.424	86	176	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:0008360	Biological Process	regulation of cell shape
GO:0009813	Biological Process	flavonoid biosynthetic process
GO:0019252	Biological Process	starch biosynthetic process
GO:0043068	Biological Process	positive regulation of programmed cell death
GO:0048316	Biological Process	seed development
GO:0048481	Biological Process	plant ovule development
GO:0080155	Biological Process	regulation of double fertilization forming a zygote and endosperm
GO:2000029	Biological Process	regulation of proanthocyanidin biosynthetic process
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:0000037	anatomy	shoot apex
PO:0009001	anatomy	fruit
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009052	anatomy	flower pedicel
PO:0020024	anatomy	endothelium
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

Sequence ? help Back to Top
Protein Sequence Length: 252 aa Download sequence Send to blast
MGRGKIEIKK IENQTARQVT FSKRRTGLIK KTRELSILCD AHIGLIVFSA TGKLSEFCSE 60 QNRMPQLIDR YLHTNGLRLP DHHDDQEQLH HEMELLRRET CNLELRLRPF HGHDLASIPP 120 NELDGLERQL EHSVLKVRER KNELMQQQLE NLSRKRRMLE EDNNNMYRWL HEHRAAMEFQ 180 QAGIDTKPGE YQQFIEQLQC YKPGEYQQFL EQQQQQPNSV LQLATLPSEI DPTYNLQLAQ 240 PNLQNDPTAQ ND

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	2e-15	1	75	1	73	MEF2C
5f28_B	2e-15	1	75	1	73	MEF2C
5f28_C	2e-15	1	75	1	73	MEF2C
5f28_D	2e-15	1	75	1	73	MEF2C
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	152	157	SRKRRM

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.31019	0.0	flower\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	249851_at	1e-166
Expression Atlas	AT5G23260	-
AtGenExpress	AT5G23260	-
ATTED-II	AT5G23260	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed during seed development.
Uniprot	TISSUE SPECIFICITY: Expressed in buds, flowers and immature seeds, but not in roots, stems, leaves, seedlings or siliques valves. Expression in seed coat is confined to the endothelium layer.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a MADS box protein. Regulates proanthocyanidin biosynthesis in the inner-most cell layer of the seed coat. Also controls cell shape of the inner-most cell layer of the seed coat. Also shown to be necessary for determining the identity of the endothelial layer within the ovule. Paralogous to GOA.
UniProt	Transcription factor involved in the developmental regulation of the endothelium and in the accumulation of proanthocyanidins (PAs) or condensed tannins which give the seed its brown pigmentation after oxidation (PubMed:12368498, PubMed:16080001). Necessary for the normal activation of the BANYULS promoter in the endothelium body (PubMed:12368498). Is required, together with AGL11/STK for the maternal control of endothelium formation, which is essential for female gametophyte development and fertilization, and seed formation (PubMed:22176531). Interacts genetically with AGL1/SHP1 and AGL5/SHP2 in a partially antagonistic manner and represses AGL1/SHP1, AGL5/SHP2, and AGL8/FUL during flower development. Is essential for the coordination of cell divisions in ovule, seed coat development and endosperm formation (PubMed:27776173). Mediates the crosstalk between endothelium and nucellus to ensure proper seed formation. Functions redundantly with AGL63/GOA to repress nucellus growth and promote its degeneration. Represses the negative regulator of autophagy and programmed cell death HVA22D in the proximal nucellus (PubMed:27233529). Binds specifically to the CArG box DNA sequence 5'-CC (A/T)6 GG-3' (PubMed:16080001). {ECO:0000269\|PubMed:12368498, ECO:0000269\|PubMed:16080001, ECO:0000269\|PubMed:22176531, ECO:0000269\|PubMed:27233529, ECO:0000269\|PubMed:27776173}.

Function -- GeneRIF ? help Back to Top
No shared protein interaction partners for ABS and GOA could be identified. [PMID: 20598091] STK and ABS played a role in the maternal control of endothelium formation, as the abs stk double mutant completely lacks endothelium. [PMID: 22176531] Study suggests that ABS is not only required for the regulation of PA accumulation in the seed coat but positively regulates coordinated cell divisions in the inner integument layer of the ovule, nuclear endosperm proliferation, endothelium cell morphology, and influences on mucilage release of the seed coat epidermal cell layer. [PMID: 27776173] the roles and mode of action of TT16 and TT15 during seed development and proanthocyanidin biosynthesis [PMID: 28830101]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G23260.2

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G61720(A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G23260, AT1G24260, AT1G31640, AT1G46408, AT1G48150, AT1G69120
IntAct	Search Q8RYD9

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G23260

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ318098	0.0	AJ318098.1 Arabidopsis thaliana mRNA for putative MADS-domain transcription factor (abs gene).

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001330404.1	0.0	K-box region and MADS-box transcription factor family protein
Refseq	NP_974823.1	0.0	K-box region and MADS-box transcription factor family protein
Swissprot	Q8RYD9	0.0	TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBL	A0A178UI66	0.0	A0A178UI66_ARATH; TT16
TrEMBL	A0A1P8BAR2	0.0	A0A1P8BAR2_ARATH; K-box region and MADS-box transcription factor family protein
STRING	AT5G23260.2	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6506	25	43
Representative plant	OGRP16	17	761

Link Out ? help Back to Top
Phytozome	AT5G23260.2
Entrez Gene	832390
iHOP	AT5G23260
wikigenes	AT5G23260

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] Becker A, et al. A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes. Mol. Genet. Genomics, 2002. 266(6): p. 942-50 [PMID:11862488] Nesi N, et al. The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell, 2002. 14(10): p. 2463-79 [PMID:12368498] R Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes. Plant J., 2002. 32(2): p. 243-53 [PMID:12383089] 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] 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] De Bodt S,Theissen G,Van de Peer Y Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting. Mol. Biol. Evol., 2006. 23(6): p. 1293-303 [PMID:16581940] 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] Popescu SC, et al. Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc. Natl. Acad. Sci. U.S.A., 2007. 104(11): p. 4730-5 [PMID:17360592] Nesi N, et al. The promoter of the Arabidopsis thaliana BAN gene is active in proanthocyanidin-accumulating cells of the Brassica napus seed coat. Plant Cell Rep., 2009. 28(4): p. 601-17 [PMID:19153740] Prasad K,Zhang X,Tob The Arabidopsis B-sister MADS-box protein, GORDITA, represses fruit growth and contributes to integument development. Plant J., 2010. 62(2): p. 203-14 [PMID:20088901] Prasad K,Ambrose BA Shaping up the fruit: control of fruit size by an Arabidopsis B-sister MADS-box gene. Plant Signal Behav, 2010. 5(7): p. 899-902 [PMID:20484990] Erdmann R,Gramzow L,Melzer R,Theissen G,Becker A GORDITA (AGL63) is a young paralog of the Arabidopsis thaliana B(sister) MADS box gene ABS (TT16) that has undergone neofunctionalization. Plant J., 2010. 63(6): p. 914-24 [PMID:20598091] Mizzotti C, et al. The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development. Plant J., 2012. 70(3): p. 409-20 [PMID:22176531] Kim K,Jiang K,Teng SL,Feldman LJ,Huang H Using biologically interrelated experiments to identify pathway genes in Arabidopsis. Bioinformatics, 2012. 28(6): p. 815-22 [PMID:22271267] 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] Rhodes DH, et al. Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm. J. Agric. Food Chem., 2014. 62(45): p. 10916-27 [PMID:25272193] 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] Xu W, et al. Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds. Plant Cell, 2016. 28(6): p. 1343-60 [PMID:27233529] 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] Coen O, et al. Developmental patterning of the sub-epidermal integument cell layer in Arabidopsis seeds. Development, 2017. 144(8): p. 1490-1497 [PMID:28348169] Xu W, et al. TRANSPARENT TESTA 16 and 15 act through different mechanisms to control proanthocyanidin accumulation in Arabidopsis testa. J. Exp. Bot., 2017. 68(11): p. 2859-2870 [PMID:28830101] Fiume E,Coen O,Xu W,Lepiniec L,Magnani E Developmental patterning of sub-epidermal cells in the outer integument of Arabidopsis seeds. PLoS ONE, 2017. 12(11): p. e0188148 [PMID:29141031]