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

Lj5g3v1473470.1

Organism

Lotus japonicus

Taxonomic ID

34305

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus

Family

NF-YC

Protein Properties

Length: 260aa MW: 28879.8 Da PI: 5.9649

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj5g3v1473470.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	175.7	4.7e-55	79	182	1	101
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdf 91 ql++fw++q i+k++dfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlrsw+h+eenkrrtl+k+diaaa+trtdifdf Lj5g3v1473470.1 79 QLQAFWANQyqeIDKVSDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDF 172 89****998999**************************************************************************** PP NF-YC 92 lvdivprdel 101 lvdivpr++l Lj5g3v1473470.1 173 LVDIVPREDL 182 *****987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	7.04E-33	59	173	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	8.6E-38	93	165	IPR009072	Histone-fold
Pfam	PF00808	1.3E-21	101	164	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:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 260 aa Download sequence Send to blast
MDHQGHGQNP SMGVGGSGPQ MTYGSNPYLQ NPLTGPPGMV VSSAGNVQST GQPVGTQMGH 60 PQLAYQHIHQ QQQQQLQQQL QAFWANQYQE IDKVSDFKNH SLPLARIKKI MKADEDVRMI 120 SAEAPVVFAR ACEMFILELT LRSWNHTEEN KRRTLQKNDI AAAITRTDIF DFLVDIVPRE 180 DLKDEVLATM PGGAMPVAGP GDGLPYCYMP PQHAQQVGPG GVMMHKPVMD PNMYAMQPDP 240 FMAPQMWLQP PEQQQSSPDH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	2e-61	86	179	2	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	151	157	RRTLQKN

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Lja.7664	0.0	cell culture\| pod\| root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269\|PubMed:11250072}.
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}.
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	Lj5g3v1473470.1

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	BT142723	0.0	BT142723.1 Lotus japonicus clone JCVI-FLLj-15C23 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015968567.1	1e-152	nuclear transcription factor Y subunit C-9
Refseq	XP_015968568.1	1e-152	nuclear transcription factor Y subunit C-9
Refseq	XP_016205500.1	1e-152	nuclear transcription factor Y subunit C-9
Refseq	XP_020959710.1	1e-152	nuclear transcription factor Y subunit C-9
Refseq	XP_025603644.1	1e-152	nuclear transcription factor Y subunit C-9
Refseq	XP_025603645.1	1e-152	nuclear transcription factor Y subunit C-9
Refseq	XP_025662538.1	1e-152	nuclear transcription factor Y subunit C-9
Refseq	XP_025662539.1	1e-152	nuclear transcription factor Y subunit C-9
Swissprot	Q8L4B2	3e-81	NFYC9_ARATH; Nuclear transcription factor Y subunit C-9
Swissprot	Q9ZVL3	3e-81	NFYC3_ARATH; Nuclear transcription factor Y subunit C-3
TrEMBL	I3SQH5	0.0	I3SQH5_LOTJA; Uncharacterized protein
STRING	AES82522	1e-150	(Medicago truncatula)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1257	34	108

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G54830.3	4e-72	nuclear factor Y, subunit C3

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] 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] 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]