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

AA39G00776

Organism

Aethionema arabicum

Taxonomic ID

228871

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Aethionemeae; Aethionema

Family

MIKC_MADS

Protein Properties

Length: 159aa MW: 18402.1 Da PI: 9.6415

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AA39G00776	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	100.9	4.7e-32	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye++s AA39G00776 9 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCS 59 79***********************************************96 PP
2	K-box	79.6	7.8e-27	93	158	16	81
K-box 16 slqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelq 81 s+qqe+ kLk++++ Lqr+qR+llGedL++Ls keL++Le+qL++slk+iR+ +++++l+q+++lq AA39G00776 93 SSQQEYLKLKERYDALQRTQRNLLGEDLGPLSTKELESLERQLDSSLKQIRALRTQFMLDQLNDLQ 158 68*************************************************************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	1.3E-41	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	33.515	1	61	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.25E-43	2	76	No hit	No description
SuperFamily	SSF55455	4.71E-34	2	77	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.4E-33	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.1E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.4E-33	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.4E-33	38	59	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	13.017	91	159	IPR002487	Transcription factor, K-box
Pfam	PF01486	6.0E-21	94	158	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0001708	Biological Process	cell fate specification
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010093	Biological Process	specification of floral organ identity
GO:0048481	Biological Process	plant ovule development
GO:0048833	Biological Process	specification of floral organ number
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

Sequence ? help Back to Top
Protein Sequence Length: 159 aa Download sequence Send to blast
MGRGRVELKR IENKINRQVT FAKRRNGLLK KAYELSVLCD AEVALIIFSN RGKLYEFCSS 60 SSMLRTLERY QKCNYGAPEP NVPSREALAV ELSSQQEYLK LKERYDALQR TQRNLLGEDL 120 GPLSTKELES LERQLDSSLK QIRALRTQFM LDQLNDLQS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ox0_A	2e-54	75	159	1	85	Developmental protein SEPALLATA 3
4ox0_B	2e-54	75	159	1	85	Developmental protein SEPALLATA 3
4ox0_C	2e-54	75	159	1	85	Developmental protein SEPALLATA 3
4ox0_D	2e-54	75	159	1	85	Developmental protein SEPALLATA 3
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor active in inflorescence development and floral organogenesis. Functions with SEPALLATA1/AGL2 and SEPALLATA2/AGL4 to ensure proper development of petals, stamens and carpels and to prevent the indeterminate growth of the flower meristem. Interacts with APETALA1, AGAMOUS or APETALA3/PISTILLATA to form complexes, that could be involved in genes regulation during floral meristem development (PubMed:10821278, PubMed:11206550). Binds specifically to the CArG box DNA sequence 5'-CC (A/T)6 GG-3' (PubMed:16080001). {ECO:0000269\|PubMed:10821278, ECO:0000269\|PubMed:11206550, ECO:0000269\|PubMed:16080001}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00605	ChIP-seq	Transfer from AT1G24260	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AA39G00776

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT033157	1e-165	BT033157.1 Arabidopsis thaliana unknown protein (At1g24260) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001185081.1	1e-110	K-box region and MADS-box transcription factor family protein
Refseq	NP_564214.2	1e-110	K-box region and MADS-box transcription factor family protein
Swissprot	O22456	1e-111	SEP3_ARATH; Developmental protein SEPALLATA 3
TrEMBL	A0A384L6U0	1e-109	A0A384L6U0_ARATH; SEP3
TrEMBL	B4F7R9	1e-109	B4F7R9_ARATH; At1g24260
TrEMBL	F4I972	1e-109	F4I972_ARATH; K-box region and MADS-box transcription factor family protein
STRING	AT1G24260.2	1e-109	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6220	26	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G24260.3	1e-113	MIKC_MADS family protein

Publications ? help Back to Top
Maejima K, et al. Recognition of floral homeotic MADS domain transcription factors by a phytoplasmal effector, phyllogen, induces phyllody. Plant J., 2014. 78(4): p. 541-54 [PMID:24597566] MacLean AM, et al. Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner. PLoS Biol., 2014. 12(4): p. e1001835 [PMID:24714165] Iglesias FM, et al. The arabidopsis DNA polymerase δ has a role in the deposition of transcriptionally active epigenetic marks, development and flowering. PLoS Genet., 2015. 11(2): p. e1004975 [PMID:25693187] He Q,Fu AY,Zhang GC,Li TJ,Zhang JH Arabidopsis thaliana SEPALLATA3 protein prokaryotic expression and purification. Cell. Mol. Biol. (Noisy-le-grand), 2015. 61(2): p. 60-3 [PMID:26025404] Maejima K, et al. Degradation of class E MADS-domain transcription factors in Arabidopsis by a phytoplasmal effector, phyllogen. Plant Signal Behav, 2015. 10(8): p. e1042635 [PMID:26179462] Muiño JM, et al. Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor. Mol. Biol. Evol., 2016. 33(1): p. 185-200 [PMID:26429922] Shi Q,Zhou J,Wang P,Lin X,Xu Y Protein expression and characterization of SEP3 from Arabidopsis thaliana. Genet. Mol. Res., 2015. 14(4): p. 12529-36 [PMID:26505403] He Q,Fu AY,Zhang GC,Li TJ,Zhang JH Cloning, Prokaryotic Expression and Purification of CpfS1 Gene from Arabidopsis Thaliana. Cell. Mol. Biol. (Noisy-le-grand), 2015. 61(8): p. 123-7 [PMID:26718440] Soza VL,Snelson CD,Hewett Hazelton KD,Di Stilio VS Partial redundancy and functional specialization of E-class SEPALLATA genes in an early-diverging eudicot. Dev. Biol., 2016. 419(1): p. 143-155 [PMID:27502434] Conn VM, et al. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants, 2017. 3: p. 17053 [PMID:28418376] Käppel S,Melzer R,Rümpler F,Gafert C,Theißen G The floral homeotic protein SEPALLATA3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS-domain. Plant J., 2018. 95(2): p. 341-357 [PMID:29744943]