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

Gh_D06G1389

Organism

Gossypium hirsutum

Taxonomic ID

3635

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

M-type_MADS

Protein Properties

Length: 175aa MW: 19701.9 Da PI: 10.6762

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_D06G1389	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	84.9	4.8e-27	31	80	2	51
---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 ri+n++ rqvtfsk rng+lKKA+ELSvLCdaeva+i fs++gkl e++s Gh_D06G1389 31 RIDNDTSRQVTFSKQRNGLLKKAFELSVLCDAEVALITFSPRGKLSEFAS 80 8***********************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	28.623	22	82	IPR002100	Transcription factor, MADS-box
SMART	SM00432	5.4E-34	22	81	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.9E-27	24	44	IPR002100	Transcription factor, MADS-box
CDD	cd00265	3.19E-40	24	96	No hit	No description
SuperFamily	SSF55455	3.27E-31	24	110	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.5E-23	31	78	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50850	9.761	41	175	IPR020846	Major facilitator superfamily domain
PRINTS	PR00404	4.9E-27	44	59	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.9E-27	59	80	IPR002100	Transcription factor, MADS-box
Pfam	PF00083	6.4E-8	81	174	IPR005828	Major facilitator, sugar transporter-like
SuperFamily	SSF103473	4.05E-6	109	174	IPR020846	Major facilitator superfamily domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0055085	Biological Process	transmembrane transport
GO:0016021	Cellular Component	integral component of membrane
GO:0003677	Molecular Function	DNA binding
GO:0022857	Molecular Function	transmembrane transporter activity
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 175 aa Download sequence Send to blast
MHVWYFIYIC FVGFEGTKIL IMVRGKEKMR RIDNDTSRQV TFSKQRNGLL KKAFELSVLC 60 DAEVALITFS PRGKLSEFAS SSMQQTIERY RRHTRDNETN NPIEQNLQLL TLFKSSLYFT 120 GIVSTFGAFY VTRNKGRRAN ILVGAVSFFL GGASNAGAVN ITMLIIGRIL LGAGI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6byy_A	1e-16	22	108	1	89	MEF2 CHIMERA
6byy_B	1e-16	22	108	1	89	MEF2 CHIMERA
6byy_C	1e-16	22	108	1	89	MEF2 CHIMERA
6byy_D	1e-16	22	108	1	89	MEF2 CHIMERA
6bz1_A	2e-16	22	108	1	89	MEF2 CHIMERA
6bz1_B	2e-16	22	108	1	89	MEF2 CHIMERA
6bz1_C	2e-16	22	108	1	89	MEF2 CHIMERA
6bz1_D	2e-16	22	108	1	89	MEF2 CHIMERA
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Ghi.12993	6e-93	boll

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}.

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}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	KC155653	1e-111	KC155653.1 Gossypium hirsutum MADS box protein MADS58 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012474816.1	3e-53	PREDICTED: MADS-box protein SOC1-like isoform X1
Refseq	XP_012474817.1	3e-53	PREDICTED: MADS-box protein SOC1-like isoform X2
Refseq	XP_012474818.1	2e-53	PREDICTED: MADS-box protein SOC1-like isoform X3
Swissprot	O64645	1e-38	SOC1_ARATH; MADS-box protein SOC1
TrEMBL	A0A0D2PBA3	3e-52	A0A0D2PBA3_GOSRA; Uncharacterized protein
STRING	Gorai.007G237300.1	9e-54	(Gossypium raimondii)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45660.1	4e-41	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]