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

Solyc08g007960.1.1

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

NF-YC

Protein Properties

Length: 125aa MW: 13990.9 Da PI: 6.9449

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc08g007960.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	100.2	1.5e-31	18	103	19	98
NF-YC 19 helPlarikkilk.adedvkmisaeaPvllskacelfileltlrswl.....haeenkrrtlkksdiaaavtrtdifdflvdivpr 98 h+lPlarikki+k + +dvkmis eaP+++skacelfi elt r+w+ + +e++r+tl+k d+a+a+ td+fdflv+ v + Solyc08g007960.1.1 18 HSLPLARIKKIMKkSSDDVKMISGEAPIVFSKACELFIEELTKRAWIimtnnNMHEKRRSTLQKDDVASAIIATDVFDFLVNLVSN 103 99********825689************************83222234567899*******************99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	1.03E-21	15	97	IPR009072	Histone-fold
Pfam	PF00808	5.5E-18	19	88	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
Gene3D	G3DSA:1.10.20.10	3.7E-29	20	102	IPR009072	Histone-fold

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 125 aa Download sequence Send to blast
MRQAGAYSGI LSRKTGPHSL PLARIKKIMK KSSDDVKMIS GEAPIVFSKA CELFIEELTK 60 RAWIIMTNNN MHEKRRSTLQ KDDVASAIIA TDVFDFLVNL VSNTTHDHNN CEELNDEESR 120 QDSP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	2e-30	18	101	16	93	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269\|PubMed:11250072}.

Functional Description ? help Back to Top
Source	Description
UniProt	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc08g007960.1.1

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	AP010260	0.0	Solanum lycopersicum DNA, chromosome 8, clone: C08SLe0010M05, complete sequence

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009628926.1	3e-55	PREDICTED: nuclear transcription factor Y subunit C-2-like
Refseq	XP_009785550.1	3e-55	PREDICTED: nuclear transcription factor Y subunit C-2-like
Refseq	XP_016485723.1	3e-55	PREDICTED: nuclear transcription factor Y subunit C-2-like
Refseq	XP_016505996.1	3e-55	PREDICTED: nuclear transcription factor Y subunit C-2-like
Swissprot	Q9ZVL3	1e-29	NFYC3_ARATH; Nuclear transcription factor Y subunit C-3
TrEMBL	A0A3Q7IF19	1e-87	A0A3Q7IF19_SOLLC; Uncharacterized protein
STRING	Solyc08g007960.1.1	2e-88	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA12881	17	20
Representative plant	OGRP315	17	117

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G54830.3	6e-32	nuclear factor Y, subunit C3

Link Out ? help Back to Top
Phytozome	Solyc08g007960.1.1

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] Hwang YH, et al. Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time. Plant Cell Rep., 2016. 35(4): p. 857-65 [PMID:26754793] Liu X, et al. The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis. Nat Commun, 2016. 7: p. 12768 [PMID:27624486] Myers ZA, et al. NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana. PLoS Genet., 2016. 12(9): p. e1006333 [PMID:27685091] Gnesutta N,Saad D,Chaves-Sanjuan A,Mantovani R,Nardini M Crystal Structure of the Arabidopsis thaliana L1L/NF-YC3 Histone-fold Dimer Reveals Specificities of the LEC1 Family of NF-Y Subunits in Plants. Mol Plant, 2017. 10(4): p. 645-648 [PMID:27871811] Tang Y, et al. Arabidopsis NF-YCs Mediate the Light-Controlled Hypocotyl Elongation via Modulating Histone Acetylation. Mol Plant, 2017. 10(2): p. 260-273 [PMID:27876642] Zhao H, et al. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. Front Plant Sci, 2016. 7: p. 2045 [PMID:28119722] Gnesutta N, et al. CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer. Plant Cell, 2017. 29(6): p. 1516-1532 [PMID:28526714]