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

Cc02_g20960

Common Name

GSCOC_T00014721001

Organism

Coffea canephora

Taxonomic ID

49390

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea

Family

MIKC_MADS

Protein Properties

Length: 265aa MW: 29734.3 Da PI: 8.3343

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cc02_g20960	genome	CGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	87.5	7.3e-28	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 kri+n + rqvtfskRr g++KKA+ELS+LCdae+a+i+fs tgkl+ey+s Cc02_g20960 9 KRIDNLTARQVTFSKRRRGLFKKAQELSTLCDAEIALIVFSATGKLFEYCS 59 79***********************************************96 PP
2	K-box	53.3	1.2e-18	85	172	12	99
K-box 12 akaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 +++++ ++ +a L +ei++ e+Rhl+Ge+L Ls+++L +Le+ +e +l++i ++K + ++++i l+kk l+een +Lr+k++ Cc02_g20960 85 HHTQRENHTHAMLAEEIKEKTAELRHLKGEELVGLSMEDLVKLEKLVEAGLSRIAKTKGDKFMKEIGILKKKAALLKEENAKLRQKVA 172 578999999*****************************************************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	29.254	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.4E-39	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	7.59E-30	3	73	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.5E-27	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
CDD	cd00265	3.13E-39	3	75	No hit	No description
Pfam	PF00319	1.4E-24	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.5E-27	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.5E-27	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	1.9E-15	85	171	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	11.675	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: 265 aa Download sequence Send to blast
MVRQRIQIKR IDNLTARQVT FSKRRRGLFK KAQELSTLCD AEIALIVFSA TGKLFEYCSS 60 SMMQVIERHR LCSEDIGRQD KHPPHHTQRE NHTHAMLAEE IKEKTAELRH LKGEELVGLS 120 MEDLVKLEKL VEAGLSRIAK TKGDKFMKEI GILKKKAALL KEENAKLRQK VAGTSEDETP 180 LLEQGISSES VTRLSDQAGS CPRDLNNSDT FLQLGEDEIA VAEDRIYNLS IAGSMMPRNC 240 SLCCIIFFKK NNMHVCQACG SLST*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	7e-19	1	104	1	91	MEF2C
5f28_B	7e-19	1	104	1	91	MEF2C
5f28_C	7e-19	1	104	1	91	MEF2C
5f28_D	7e-19	1	104	1	91	MEF2C
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription repressor that inhibit floral transition in the autonomous flowering pathway, independent of photoperiod and temperature. Acts in a dosage-dependent manner. Together with AGL24 and AP1, controls the identity of the floral meristem and regulates expression of class B, C and E genes. Promotes EFM expression to suppress flowering (PubMed:25132385). {ECO:0000269\|PubMed:16679456, ECO:0000269\|PubMed:18694458, ECO:0000269\|PubMed:19656343, ECO:0000269\|PubMed:25132385}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by the floral homeotic genes AP1 and SEP3 in emerging floral meristems. Up-regulated by HUA2. {ECO:0000269\|PubMed:15659097, ECO:0000269\|PubMed:17428825, ECO:0000269\|PubMed:18694458}.

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	KJ483242	0.0	KJ483242.1 Coffea arabica SVP-3 (SVP-3) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027160324.1	0.0	MADS-box protein SVP-like isoform X1
Refseq	XP_027160325.1	0.0	MADS-box protein SVP-like isoform X1
Refseq	XP_027160326.1	0.0	MADS-box protein SVP-like isoform X1
Swissprot	Q9FVC1	5e-66	SVP_ARATH; MADS-box protein SVP
TrEMBL	A0A068TMY7	0.0	A0A068TMY7_COFCA; Uncharacterized protein
STRING	PGSC0003DMT400083739	1e-77	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA938	23	77

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G22540.1	3e-60	MIKC_MADS family protein

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] Jaudal M, et al. Overexpression of Medicago SVP genes causes floral defects and delayed flowering in Arabidopsis but only affects floral development in Medicago. J. Exp. Bot., 2014. 65(2): p. 429-42 [PMID:24249713] Müller-Xing R,Clarenz O,Pokorny L,Goodrich J,Schubert D Polycomb-Group Proteins and FLOWERING LOCUS T Maintain Commitment to Flowering in Arabidopsis thaliana. Plant Cell, 2014. 26(6): p. 2457-2471 [PMID:24920331] Hwan Lee J,Sook Chung K,Kim SK,Ahn JH Post-translational regulation of SHORT VEGETATIVE PHASE as a major mechanism for thermoregulation of flowering. Plant Signal Behav, 2014. 9(4): p. e28193 [PMID:25764420] Chen Z, et al. Overexpression of AtAP1M3 regulates flowering time and floral development in Arabidopsis and effects key flowering-related genes in poplar. Transgenic Res., 2015. 24(4): p. 705-15 [PMID:25820621] Wells CE,Vendramin E,Jimenez Tarodo S,Verde I,Bielenberg DG A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]. BMC Plant Biol., 2015. 15: p. 41 [PMID:25848674] Müller-Xing R,Schubert D,Goodrich J Non-inductive conditions expose the cryptic bract of flower phytomeres in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(4): p. e1010868 [PMID:25924005] Marín-González E, et al. SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures. Plant Physiol., 2015. 169(2): p. 1214-24 [PMID:26243615] Bechtold U, et al. Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis. Plant Cell, 2016. 28(2): p. 345-66 [PMID:26842464] Fernández V,Takahashi Y,Le Gourrierec J,Coupland G Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days. Plant J., 2016. 86(5): p. 426-40 [PMID:27117775] 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] Zou YP, et al. Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol., 2017. 18(1): p. 239 [PMID:29284515] Richter R, et al. Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications. PLoS Genet., 2019. 15(4): p. e1008065 [PMID:30946745]