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_009110863.1

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: 218aa MW: 24412.4 Da PI: 6.1499

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009110863.1	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	4.1e-56	47	150	1	101
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdfl 92 ql++fw++q ie++tdfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlrsw+h+eenkrrtl+k+diaaavtrtdifdfl XP_009110863.1 47 QLQVFWQNQfkeIENTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAVTRTDIFDFL 141 89****99999****************************************************************************** PP NF-YC 93 vdivprdel 101 vdivpr++l XP_009110863.1 142 VDIVPREDL 150 ****986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	3.19E-33	8	141	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	6.0E-38	61	133	IPR009072	Histone-fold
Pfam	PF00808	5.2E-22	69	132	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain

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: 218 aa Download sequence Send to blast
MDQQEHGQSR AMNYGTNPYQ TGSVGPTAPS GQMAFHQHHQ QQQLTQQLQV FWQNQFKEIE 60 NTTDFKNHSL PLARIKKIMK ADEDVRMISA EAPVVFARAC EMFILELTLR SWNHTEENKR 120 RTLQKNDIAA AVTRTDIFDF LVDIVPREDL RDEVLGSIPR GTVPEASAAG YPYGYLPSGT 180 APVGNAGMVM GNPGSAYPPN LYMGQPMWQH QGPGQPDQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	1e-63	55	147	3	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	119	125	RRTLQKN

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_009110863.1

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	AK316882	1e-173	AK316882.2 Arabidopsis thaliana AT1G08970 mRNA, complete cds, clone: RAFL14-04-L24.
GenBank	AY085860	1e-173	AY085860.1 Arabidopsis thaliana clone 1911 mRNA, complete sequence.
GenBank	AY126997	1e-173	AY126997.1 Arabidopsis thaliana At1g08970/F7G19_16 mRNA, complete cds.
GenBank	AY143827	1e-173	AY143827.1 Arabidopsis thaliana At1g08970/F7G19_16 mRNA, complete cds.
GenBank	CP002684	1e-173	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
GenBank	F7G19	1e-173	AC000106.1 Sequence of BAC F7G19 from Arabidopsis thaliana chromosome 1, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009110863.1	1e-165	PREDICTED: nuclear transcription factor Y subunit C-9-like
Refseq	XP_009110864.1	1e-165	PREDICTED: nuclear transcription factor Y subunit C-9-like
Refseq	XP_009110865.1	1e-165	PREDICTED: nuclear transcription factor Y subunit C-9-like
Swissprot	Q8L4B2	1e-125	NFYC9_ARATH; Nuclear transcription factor Y subunit C-9
TrEMBL	M4EPM9	1e-163	M4EPM9_BRARP; Uncharacterized protein
STRING	Bra030749.1-P	1e-164	(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	1e-115	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]