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

Potri.003G124500.1

Common Name

POPTR_0003s12460g

Organism

Populus trichocarpa

Taxonomic ID

3694

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus

Family

NF-YC

Protein Properties

Length: 118aa MW: 12806.8 Da PI: 8.5127

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Potri.003G124500.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	112.3	2.6e-35	22	102	19	98
NF-YC 19 helPlarikkilk.adedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdflvdivpr 98 h+lPlarikki+k + +dvkmis eaP+++skacelfi elt rsw+ + + krrtl+k d+a+avt tdifdflv+ v + Potri.003G124500.1 22 HSLPLARIKKIMKkSGDDVKMISGEAPIVFSKACELFIEELTQRSWMITIQGKRRTLHKEDVASAVTATDIFDFLVNLVSN 102 99********825689********************************************************99976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	4.77E-27	18	96	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	6.8E-32	18	88	IPR009072	Histone-fold
Pfam	PF00808	9.1E-22	23	87	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: 118 aa Download sequence Send to blast
MRQAGTYSGI LSGGLSGKTG PHSLPLARIK KIMKKSGDDV KMISGEAPIV FSKACELFIE 60 ELTQRSWMIT IQGKRRTLHK EDVASAVTAT DIFDFLVNLV SNSSHSMDIN PVEIENN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	6e-34	22	100	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	Probable transcription factor involved in the regulation of flowering time under long day (LD) conditions. Functions as repressor of flowering, independently of HD1 and GHD7. Controls flowering time by negatively regulating the expression of EHD1 and HD3A (PubMed:26542958). Component of the NF-Y/HAP transcription factor complex (By similarity). {ECO:0000250, ECO:0000269\|PubMed:26542958}.
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	Potri.003G124500.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Circadian-regulation under long day (LD) conditions. Expression increases in the middle of daytime, peaks around the end of the light period and gradually decreases during the dark period and beginning of daylight. {ECO:0000269\|PubMed:26542958}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002304485.2	1e-82	nuclear transcription factor Y subunit C-3
Swissprot	Q655V5	2e-32	NFYC4_ORYSJ; Nuclear transcription factor Y subunit C-4
Swissprot	Q9ZVL3	2e-32	NFYC3_ARATH; Nuclear transcription factor Y subunit C-3
TrEMBL	B9GWG1	3e-81	B9GWG1_POPTR; Uncharacterized protein
STRING	POPTR_0001s09100.1	4e-71	(Populus trichocarpa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF10559	28	41
Representative plant	OGRP315	17	117

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G54830.3	8e-35	nuclear factor Y, subunit C3

Link Out ? help Back to Top
Phytozome	Potri.003G124500.1
Entrez Gene	7458162

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Kim SK, et al. OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice. Planta, 2016. 243(3): p. 563-76 [PMID:26542958] 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]