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

XP_009143158.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

MIKC_MADS

Protein Properties

Length: 213aa MW: 24399.9 Da PI: 9.6541

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009143158.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	92.2	2.6e-29	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaev++iifs++ klye++s XP_009143158.1 9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVSLIIFSPKAKLYEFAS 59 79***********************************************86 PP
2	K-box	96	5.9e-32	77	171	4	98
K-box 4 ssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 s+k ++e++ ++l++e+a++ k+ie+L+ ++R+llGe+++s+s++eLqq+eqqLeks+k iR++K+++++eqie+l++kek+l enk+L++k+ XP_009143158.1 77 VSTKPVSEENLQHLKHEAANMMKKIEQLEASKRKLLGEGIGSCSIEELQQIEQQLEKSVKCIRARKTQVFKEQIEQLKQKEKALAAENKKLTEKW 171 566779**************************************************************************************997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	31.048	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.8E-39	1	60	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.4E-30	3	23	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	7.33E-33	3	83	IPR002100	Transcription factor, MADS-box
CDD	cd00265	2.71E-40	3	78	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.3E-25	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.4E-30	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.4E-30	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	3.0E-29	85	170	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.907	87	177	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: 213 aa Download sequence Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVSLIIFSP KAKLYEFASS 60 NMQDTIDRYL RHTKDRVSTK PVSEENLQHL KHEAANMMKK IEQLEASKRK LLGEGIGSCS 120 IEELQQIEQQ LEKSVKCIRA RKTQVFKEQI EQLKQKEKAL AAENKKLTEK WGSHEIEVWS 180 NKNQESGKGD EESSPSSEVE TELFIGLPCS SRK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6bz1_A	4e-19	1	94	1	95	MEF2 CHIMERA
6bz1_B	4e-19	1	94	1	95	MEF2 CHIMERA
6bz1_C	4e-19	1	94	1	95	MEF2 CHIMERA
6bz1_D	4e-19	1	94	1	95	MEF2 CHIMERA
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Rapidly up-regulated in apical meristems during the transition to flowering. Transiently expressed in inflorescence meristem. Re-appears in stage 3 flowers, in the central dome that later will develop into stamens and carpels. {ECO:0000269\|PubMed:19656343}.
Uniprot	TISSUE SPECIFICITY: Widely expressed. Not found in the apical meristem of short-day grown plants in vegetative stage.

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}.

Function -- GeneRIF ? help Back to Top
SOC1 influences flowering time, lateral branching, oil quality, and seed yield in Brassica. [PMID: 29943206]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009143158.1

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	JQ845923	0.0	JQ845923.1 Brassica juncea cultivar BIO-902 MADS box transcription factor SOC1 variant 6 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009143158.1	1e-154	PREDICTED: MADS-box protein SOC1
Refseq	XP_013748134.1	1e-154	MADS-box protein SOC1
Refseq	XP_022561507.1	1e-154	MADS-box protein SOC1
Refseq	XP_022574682.1	1e-154	MADS-box protein SOC1 isoform X1
Refseq	XP_022574683.1	1e-154	MADS-box protein SOC1 isoform X1
Swissprot	O64645	1e-140	SOC1_ARATH; MADS-box protein SOC1
TrEMBL	A0A3G5BC88	1e-153	A0A3G5BC88_BRARC; MADS-box protein SOC1
TrEMBL	M4CL42	1e-153	M4CL42_BRARP; Uncharacterized protein
TrEMBL	V9LZT3	1e-153	V9LZT3_BRACM; MADS box transcription factor SOC1
TrEMBL	V9M082	1e-153	V9M082_BRAJU; MADS box transcription factor SOC1 variant 6
TrEMBL	V9M0Z7	1e-153	V9M0Z7_BRANA; MADS box transcription factor SOC1
STRING	Bra004928.1-P	1e-154	(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-111	AGAMOUS-like 20

Link Out ? help Back to Top
Entrez Gene	103866913

Publications ? help Back to Top
Kim JS, et al. A sequence-tagged linkage map of Brassica rapa. Genetics, 2006. 174(1): p. 29-39 [PMID:16988107] 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] Sri T,Mayee P,Singh A Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas. Dev. Genes Evol., 2015. 225(5): p. 287-303 [PMID:26276216] 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] Tyagi S, et al. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 influences flowering time, lateral branching, oil quality, and seed yield in Brassica juncea cv. Varuna. Funct. Integr. Genomics, 2019. 19(1): p. 43-60 [PMID:29943206]