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_009149806.1

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

NF-YC

Protein Properties

Length: 221aa MW: 24244.4 Da PI: 4.848

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009149806.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	179.1	4.2e-56	37	141	1	102
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdfl 92 ql++fw++q ie+++dfknh+lPlarikki+kadedv+misaeaP+l++kacelfilelt+rswlhaeenkrrtl+k+diaaa+trtdifdfl XP_009149806.1 37 QLQMFWSYQrqeIEQVNDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFL 131 89***998899****************************************************************************** PP NF-YC 93 vdivprdelk 102 vdivpr+e+k XP_009149806.1 132 VDIVPREEIK 141 ****9975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	6.68E-34	31	131	IPR009072	Histone-fold
Pfam	PF00808	1.4E-20	59	122	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
Gene3D	G3DSA:1.10.20.10	6.1E-37	60	137	IPR009072	Histone-fold

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

Sequence ? help Back to Top
Protein Sequence Length: 221 aa Download sequence Send to blast
MDNSNQQSSP SAAGIPPPVS AVGGASYHHL LQQQQQQLQM FWSYQRQEIE QVNDFKNHQL 60 PLARIKKIMK ADEDVRMISA EAPILFAKAC ELFILELTIR SWLHAEENKR RTLQKNDIAA 120 AITRTDIFDF LVDIVPREEI KEEPGIGGMM PPAVSGVPYY YPPMGGPGGM MIGRPAMDPS 180 GVYVQPPSQA WQSVWQTSAT GDDVSYGSGG SGGQGNLDGQ V

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	3e-55	45	137	3	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	109	115	RRTLQKN

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitous. Present in etiolated seedlings. {ECO:0000269\|PubMed:11250072, ECO:0000269\|PubMed:17322342}.

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 (By similarity). Involved in the abscisic acid (ABA) signaling pathway. {ECO:0000250, ECO:0000269\|PubMed:17322342}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009149806.1

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	KC797141	0.0	KC797141.1 Brassica napus transcription factor subunit NF-YC1 (NF-YC1) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009149806.1	1e-164	PREDICTED: nuclear transcription factor Y subunit C-1
Refseq	XP_013727066.1	1e-164	nuclear transcription factor Y subunit C-1
Swissprot	Q9FMV5	1e-113	NFYC4_ARATH; Nuclear transcription factor Y subunit C-4
TrEMBL	A0A078F4Z7	1e-162	A0A078F4Z7_BRANA; BnaA06g16420D protein
TrEMBL	A0A3P5YZS1	1e-162	A0A3P5YZS1_BRACM; Uncharacterized protein
TrEMBL	M4DNF9	1e-162	M4DNF9_BRARP; Uncharacterized protein
STRING	Bra018046.1-P	1e-163	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM478	28	160

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G63470.2	8e-99	nuclear factor Y, subunit C4

Publications ? help Back to Top
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] 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] Qi M, et al. QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnol. J., 2019. 17(1): p. 252-263 [PMID:29878511]