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

evm_27.model.AmTr_v1.0_scaffold00039.13

Common Name

AMTR_s00039p00040000, LOC18444019

Organism

Amborella trichopoda

Taxonomic ID

13333

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella

Family

NF-YC

Protein Properties

Length: 274aa MW: 29911.9 Da PI: 6.5117

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00039.13	genome	TAGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	179.6	2.8e-56	82	186	1	102
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhae 67 ql+ fw++q ie++tdfknh+lPlarikki+kadedv+misaeaPv+++kace+fileltlrsw+h+e evm_27.model.AmTr_v1.0_scaffold00039.13 82 QLQLFWANQlqeIEQTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFAKACEMFILELTLRSWIHTE 151 89****99999***************************************************** PP NF-YC 68 enkrrtlkksdiaaavtrtdifdflvdivprdelk 102 enkrrtl+k+diaaa+trtdifdflvdivprdelk evm_27.model.AmTr_v1.0_scaffold00039.13 152 ENKRRTLQKNDIAAAITRTDIFDFLVDIVPRDELK 186 ******************************975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	3.86E-33	72	176	IPR009072	Histone-fold
Pfam	PF00808	1.8E-21	104	167	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
Gene3D	G3DSA:1.10.20.10	1.2E-37	105	182	IPR009072	Histone-fold

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: 274 aa Download sequence Send to blast
MDHQQGQGQQ PPPVMGMVTG APPPMPYPSY QTSQVVGATS AGPGSPLGQV GPAQFGTSAP 60 HLQHPLAYQH LQHQQQAQQA HQLQLFWANQ LQEIEQTTDF KNHSLPLARI KKIMKADEDV 120 RMISAEAPVV FAKACEMFIL ELTLRSWIHT EENKRRTLQK NDIAAAITRT DIFDFLVDIV 180 PRDELKDEVI AAGLPRPAGP GLAVGGPPTD AMPYYYMPAQ APPPNVATMV GRPVGEQGLY 240 GQQPRPFVGQ QVWPTQPNQQ QQQVPEQGRG NSG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	1e-60	90	182	3	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	154	160	RRTLQKN

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}.

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_006854260.1	0.0	nuclear transcription factor Y subunit C-2
Swissprot	Q8L4B2	4e-72	NFYC9_ARATH; Nuclear transcription factor Y subunit C-9
TrEMBL	U5D2T5	0.0	U5D2T5_AMBTC; Uncharacterized protein
STRING	ERN15727	0.0	(Amborella trichopoda)

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

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G56170.2	7e-68	nuclear factor Y, subunit C2

Link Out ? help Back to Top
Phytozome	evm_27.model.AmTr_v1.0_scaffold00039.13
Entrez Gene	18444019

Publications ? help Back to Top
Amborella Genome Project The Amborella genome and the evolution of flowering plants. Science, 2013. 342(6165): p. 1241089 [PMID:24357323] 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]