PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

MIKC_MADS

Protein Properties

Length: 206aa MW: 23629 Da PI: 9.4362

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01485.1_g00004.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	95.5	2.3e-30	2	52	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaev++iifss+gklye++s Rsa1.0_01485.1_g00004.1 2 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVSLIIFSSKGKLYEFAS 52 79***********************************************86 PP
2	K-box	94.6	1.7e-31	70	164	4	98
K-box 4 ssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqe 89 s+k ++e+++++l++e+a++ k+ie+L+ ++R+llGe+++s+s++eLq++e+qLeks+k iR++K+++++eqie+l++kek l Rsa1.0_01485.1_g00004.1 70 ISNKPVSEENMQHLKHEAANMMKKIEQLEASKRKLLGEGIGSCSIEELQHIETQLEKSVKCIRARKTQVFKEQIEQLKQKEKTLAA 155 677789****************************************************************************** PP K-box 90 enkaLrkkl 98 en++L +k+ Rsa1.0_01485.1_g00004.1 156 ENQKLIEKW 164 ***9987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00265	4.74E-38	1	69	No hit	No description
SMART	SM00432	3.9E-32	1	53	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	4.97E-31	1	76	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	29.184	1	54	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	8.4E-26	3	50	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.6E-19	16	31	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.6E-19	31	52	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	3.0E-28	77	163	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.276	80	170	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: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: 206 aa Download sequence Send to blast
MKRIENATSR QVTFSKRRNG LLKKAFELSV LCDAEVSLII FSSKGKLYEF ASSNMQDTID 60 RYLTHTKDRI SNKPVSEENM QHLKHEAANM MKKIEQLEAS KRKLLGEGIG SCSIEELQHI 120 ETQLEKSVKC IRARKTQVFK EQIEQLKQKE KTLAAENQKL IEKWGSHEIE VWSKKKQESG 180 RGDEESSPSS EVETELFIGL PSSSRK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1egw_A	8e-18	1	62	7	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_B	8e-18	1	62	7	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_C	8e-18	1	62	7	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_D	8e-18	1	62	7	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
3kov_A	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3kov_B	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3kov_I	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3kov_J	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3mu6_A	6e-18	1	65	7	71	Myocyte-specific enhancer factor 2A
3mu6_B	6e-18	1	65	7	71	Myocyte-specific enhancer factor 2A
3mu6_C	6e-18	1	65	7	71	Myocyte-specific enhancer factor 2A
3mu6_D	6e-18	1	65	7	71	Myocyte-specific enhancer factor 2A
3p57_A	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3p57_B	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3p57_C	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3p57_D	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3p57_I	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
3p57_J	1e-17	1	62	7	68	Myocyte-specific enhancer factor 2A
6bz1_A	1e-17	1	62	8	69	MEF2 CHIMERA
6bz1_B	1e-17	1	62	8	69	MEF2 CHIMERA
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator active in flowering time control. May integrate signals from the photoperiod, vernalization and autonomous floral induction pathways. Can modulate class B and C homeotic genes expression. When associated with AGL24, mediates effect of gibberellins on flowering under short-day conditions, and regulates the expression of LEAFY (LFY), which links floral induction and floral development. {ECO:0000269\|PubMed:10995392, ECO:0000269\|PubMed:18339670, ECO:0000269\|PubMed:18466303, ECO:0000269\|PubMed:19656343}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_01485.1_g00004.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by gibberellins, vernalization and under long-day conditions. Gradual increase during vegetative growth. Induced by AGL24 at the shoot apex at the floral transitional stage. Repressed by SVP during the early stages of flower development. Inhibited by AP1 in emerging floral meristems (PubMed:17428825, PubMed:18339670, PubMed:19656343). Repressed by SHL to prevent flowering (PubMed:25281686). {ECO:0000269\|PubMed:17428825, ECO:0000269\|PubMed:18339670, ECO:0000269\|PubMed:19656343, ECO:0000269\|PubMed:25281686}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JQ845941	0.0	JQ845941.1 Brassica carinata cultivar NCP-9 MADS box transcription factor SOC1 variant 4 mRNA, complete cds.
GenBank	SAU25696	0.0	U25696.1 Sinapis alba transcription factor SaMADS A mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018478944.1	1e-148	PREDICTED: MADS-box protein SOC1-like
Refseq	XP_018478945.1	1e-148	PREDICTED: MADS-box protein SOC1-like
Swissprot	O64645	1e-127	SOC1_ARATH; MADS-box protein SOC1
TrEMBL	A0A3P6A828	1e-136	A0A3P6A828_BRACM; Uncharacterized protein
TrEMBL	I6SJF1	1e-136	I6SJF1_BRANA; MADS-box protein AGL20/SOC1
STRING	Bra000393.1-P	1e-135	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM78	28	413

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45660.1	1e-117	AGAMOUS-like 20

Publications ? help Back to Top
Ramamoorthy R,Phua EE,Lim SH,Tan HT,Kumar PP Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae). PLoS ONE, 2013. 8(6): p. e67243 [PMID:23840638] Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A. PLoS ONE, 2013. 8(7): p. e67987 [PMID:23976921] Mouhu K, et al. The Fragaria vesca homolog of suppressor of overexpression of constans1 represses flowering and promotes vegetative growth. Plant Cell, 2013. 25(9): p. 3296-310 [PMID:24038650] Lei HJ, et al. Identification and characterization of FaSOC1, a homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from strawberry. Gene, 2013. 531(2): p. 158-67 [PMID:24055423] Fu J, et al. Photoperiodic control of FT-like gene ClFT initiates flowering in Chrysanthemum lavandulifolium. Plant Physiol. Biochem., 2014. 74: p. 230-8 [PMID:24316581] Steinbach Y,Hennig L Arabidopsis MSI1 functions in photoperiodic flowering time control. Front Plant Sci, 2014. 5: p. 77 [PMID:24639681] Preston JC,Jorgensen SA,Jha SG Functional characterization of duplicated Suppressor of Overexpression of Constans 1-like genes in petunia. PLoS ONE, 2014. 9(5): p. e96108 [PMID:24787903] Berr A,Shafiq S,Pinon V,Dong A,Shen WH The trxG family histone methyltransferase SET DOMAIN GROUP 26 promotes flowering via a distinctive genetic pathway. Plant J., 2015. 81(2): p. 316-28 [PMID:25409787] Leal Valentim F, et al. A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network. PLoS ONE, 2015. 10(2): p. e0116973 [PMID:25719734] Ma X, et al. CYCLIN-DEPENDENT KINASE G2 regulates salinity stress response and salt mediated flowering in Arabidopsis thaliana. Plant Mol. Biol., 2015. 88(3): p. 287-99 [PMID:25948280] Kang MY, et al. Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis. Sci Rep, 2015. 5: p. 9728 [PMID:25962685] Wang C,Dehesh K From retrograde signaling to flowering time. Plant Signal Behav, 2015. 10(6): p. e1022012 [PMID:26098376] Lee JH,Jung JH,Park CM INDUCER OF CBF EXPRESSION 1 integrates cold signals into FLOWERING LOCUS C-mediated flowering pathways in Arabidopsis. Plant J., 2015. 84(1): p. 29-40 [PMID:26248809] Lee JH,Park CM Integration of photoperiod and cold temperature signals into flowering genetic pathways in Arabidopsis. Plant Signal Behav, 2015. 10(11): p. e1089373 [PMID:26430754] Li M, et al. DELLA proteins interact with FLC to repress flowering transition. J Integr Plant Biol, 2016. 58(7): p. 642-55 [PMID:26584710] Franks SJ, et al. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa. PeerJ, 2015. 3: p. e1339 [PMID:26644966] Liu B, et al. Interplay of the histone methyltransferases SDG8 and SDG26 in the regulation of transcription and plant flowering and development. Biochim. Biophys. Acta, 2016. 1859(4): p. 581-90 [PMID:26854085] Liu XR, et al. Overexpression of an Orchid (Dendrobium nobile) SOC1/TM3-Like Ortholog, DnAGL19, in Arabidopsis Regulates HOS1-FT Expression. Front Plant Sci, 2016. 7: p. 99 [PMID:26904066] Davin N, et al. Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants. Plant J., 2016. 86(5): p. 376-90 [PMID:26952251] Del Olmo I, et al. Arabidopsis DNA polymerase ϵ recruits components of Polycomb repressor complex to mediate epigenetic gene silencing. Nucleic Acids Res., 2016. 44(12): p. 5597-614 [PMID:26980282] Mahrez W, et al. BRR2a Affects Flowering Time via FLC Splicing. PLoS Genet., 2016. 12(4): p. e1005924 [PMID:27100965] Hyun Y, et al. Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Dev. Cell, 2016. 37(3): p. 254-66 [PMID:27134142] He L, et al. Maize OXIDATIVE STRESS2 Homologs Enhance Cadmium Tolerance in Arabidopsis through Activation of a Putative SAM-Dependent Methyltransferase Gene. Plant Physiol., 2016. 171(3): p. 1675-85 [PMID:27208260] Alter P, et al. Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1. Plant Physiol., 2016. 172(1): p. 389-404 [PMID:27457125] Xu C,Yu Y,Zhang Y,Li Y,Wei S Gibberellins are involved in effect of near-null magnetic field on Arabidopsis flowering. Bioelectromagnetics, 2017. 38(1): p. 1-10 [PMID:27598690] Riboni M,Robustelli Test A,Galbiati M,Tonelli C,Conti L ABA-dependent control of GIGANTEA signalling enables drought escape via up-regulation of FLOWERING LOCUS T in Arabidopsis thaliana. J. Exp. Bot., 2016. 67(22): p. 6309-6322 [PMID:27733440] Kong X,Luo X,Qu GP,Liu P,Jin JB Arabidopsis SUMO protease ASP1 positively regulates flowering time partially through regulating FLC stability . J Integr Plant Biol, 2017. 59(1): p. 15-29 [PMID:27925396] Kapolas G, et al. APRF1 promotes flowering under long days in Arabidopsis thaliana. Plant Sci., 2016. 253: p. 141-153 [PMID:27968983] Li H, et al. BZR1 Positively Regulates Freezing Tolerance via CBF-Dependent and CBF-Independent Pathways in Arabidopsis. Mol Plant, 2017. 10(4): p. 545-559 [PMID:28089951] Chen J, et al. Suppressor of Overexpression of CO 1 Negatively Regulates Dark-Induced Leaf Degreening and Senescence by Directly Repressing Pheophytinase and Other Senescence-Associated Genes in Arabidopsis. Plant Physiol., 2017. 173(3): p. 1881-1891 [PMID:28096189] Denis E, et al. WOX14 promotes bioactive gibberellin synthesis and vascular cell differentiation in Arabidopsis. Plant J., 2017. 90(3): p. 560-572 [PMID:28218997] Nasim Z,Fahim M,Ahn JH Possible Role of MADS AFFECTING FLOWERING 3 and B-BOX DOMAIN PROTEIN 19 in Flowering Time Regulation of Arabidopsis Mutants with Defects in Nonsense-Mediated mRNA Decay. Front Plant Sci, 2017. 8: p. 191 [PMID:28261246] Wilson DC,Kempthorne CJ,Carella P,Liscombe DK,Cameron RK Age-Related Resistance in Arabidopsis thaliana Involves the MADS-Domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae. Mol. Plant Microbe Interact., 2017. 30(11): p. 919-929 [PMID:28812948] Zhang GZ, et al. Ectopic expression of UGT84A2 delayed flowering by indole-3-butyric acid-mediated transcriptional repression of ARF6 and ARF8 genes in Arabidopsis. Plant Cell Rep., 2017. 36(12): p. 1995-2006 [PMID:29027578] Jamge S,Stam M,Angenent GC,Immink RGH A cautionary note on the use of chromosome conformation capture in plants. Plant Methods, 2017. 13: p. 101 [PMID:29177001] Dotto M,Gómez MS,Soto MS,Casati P UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana. Plant Cell Environ., 2018. 41(6): p. 1394-1406 [PMID:29447428]