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_009118332.1

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: 228aa MW: 25421.5 Da PI: 4.8893

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009118332.1	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	4.3e-56	55	158	1	101
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdfl 92 ql++fwe+q iek+tdfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlrsw+h+eenkrrtl+k+diaaavtrtdifdfl XP_009118332.1 55 QLQVFWENQfkeIEKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAVTRTDIFDFL 149 89****99999****************************************************************************** PP NF-YC 93 vdivprdel 101 vdivpr++l XP_009118332.1 150 VDIVPREDL 158 ****986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	2.18E-32	45	149	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	6.7E-38	69	141	IPR009072	Histone-fold
Pfam	PF00808	5.7E-22	77	140	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0005829	Cellular Component	cytosol
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 228 aa Download sequence Send to blast
MDQQEHAQSG AMNYGSNPYQ TNPMTTTSAG PAAPPGQLGF HQIHQQQQQQ QLAQQLQVFW 60 ENQFKEIEKT TDFKNHSLPL ARIKKIMKAD EDVRMISAEA PVVFARACEM FILELTLRSW 120 NHTEENKRRT LQKNDIAAAV TRTDIFDFLV DIVPREDLRD EVLGSIPRGT VPEAAAAGYP 180 YGYLPAGTAP IGNPGMVMGN PGGAYPPNPY MGQPMWQQQG PDQPDQEN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	3e-64	62	155	2	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	127	133	RRTLQKN

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.1351	0.0	bud\| flower\| leaf\| root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitous. Present in etiolated seedlings. {ECO:0000269\|PubMed:11867211, 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). Interacts with REF6 to directly regulate SOC1 transcription in response to flowering signals from photoperiod and gibberellic acid pathways (PubMed:25105952). {ECO:0000250, ECO:0000269\|PubMed:25105952}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009118332.1

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	KC797144	0.0	KC797144.1 Brassica napus transcription factor subunit NF-YC9A (NF-YC9A) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009118332.1	1e-171	PREDICTED: nuclear transcription factor Y subunit C-9
Refseq	XP_013672609.1	1e-171	nuclear transcription factor Y subunit C-9
Refseq	XP_022547296.1	1e-171	nuclear transcription factor Y subunit C-9
Swissprot	Q8L4B2	1e-138	NFYC9_ARATH; Nuclear transcription factor Y subunit C-9
TrEMBL	A0A397Y5A6	1e-169	A0A397Y5A6_BRACM; Uncharacterized protein
TrEMBL	A0A3N6S731	1e-169	A0A3N6S731_BRACR; Uncharacterized protein
TrEMBL	M4ES73	1e-169	M4ES73_BRARP; Uncharacterized protein
TrEMBL	W8EDQ7	1e-169	W8EDQ7_BRANA; Transcription factor subunit NF-YC9A
STRING	Bra031651.1-P	1e-170	(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
AT1G08970.4	3e-95	nuclear factor Y, subunit C9

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] 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] Bi C,Ma Y,Wang XF,Zhang DP Overexpression of the transcription factor NF-YC9 confers abscisic acid hypersensitivity in Arabidopsis. Plant Mol. Biol., 2017. 95(4-5): p. 425-439 [PMID:28924726] Liu X, et al. Temporal-Specific Interaction of NF-YC and CURLY LEAF during the Floral Transition Regulates Flowering. Plant Physiol., 2018. 177(1): p. 105-114 [PMID:29599268]