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

Carubv10020932m

Common Name

CARUB_v10020932mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella

Family

NF-YC

Protein Properties

Length: 219aa MW: 24366.2 Da PI: 4.7457

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10020932m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	178.6	5.9e-56	48	151	1	101
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdf 91 ql+sfwe+q iek+tdfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlrsw+h+eenkrrtl+k+diaaavtrtdifdf Carubv10020932m 48 QLQSFWETQfkeIEKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAVTRTDIFDF 141 89***999999***************************************************************************** PP NF-YC 92 lvdivprdel 101 lvdivpr++l Carubv10020932m 142 LVDIVPREDL 151 *****986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	3.22E-33	15	142	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	6.1E-38	62	134	IPR009072	Histone-fold
Pfam	PF00808	5.2E-22	70	133	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: 219 aa Download sequence Send to blast
MDQQGQSSAM NYGSNPYQTN PMTTAPAGSD HPAYHQIHQQ QQQQLTQQLQ SFWETQFKEI 60 EKTTDFKNHS LPLARIKKIM KADEDVRMIS AEAPVVFARA CEMFILELTL RSWNHTEENK 120 RRTLQKNDIA AAVTRTDIFD FLVDIVPRED LRDEVLGGVG GAEAATAAGY PYGYLPPGTA 180 PIGNPGMVMG NPGAYPPNPY MGQPMWQQQG PEQQDPDN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	4e-65	55	148	2	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	120	126	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. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10020932m

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	AC064840	0.0	AC064840.2 Arabidopsis thaliana chromosome I BAC T24C10 genomic sequence, complete sequence.
GenBank	AC069144	0.0	AC069144.9 Arabidopsis thaliana chromosome 1 BAC F14C21 genomic sequence, complete sequence.
GenBank	AY062775	0.0	AY062775.1 Arabidopsis thaliana Unknown protein (At1g54830; T22H22.22) mRNA, complete cds.
GenBank	AY081654	0.0	AY081654.1 Arabidopsis thaliana unknown protein (At1g54830) mRNA, complete cds.
GenBank	AY087517	0.0	AY087517.1 Arabidopsis thaliana clone 36272 mRNA, complete sequence.
GenBank	CP002684	0.0	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
GenBank	T22H22	0.0	AC005388.1 Sequence of BAC T22H22 from Arabidopsis thaliana chromosome 1, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006302805.1	1e-164	nuclear transcription factor Y subunit C-3
Swissprot	Q9ZVL3	1e-144	NFYC3_ARATH; Nuclear transcription factor Y subunit C-3
TrEMBL	R0IFY3	1e-162	R0IFY3_9BRAS; Uncharacterized protein
STRING	Cagra.0445s0002.1.p	1e-163	(Capsella grandiflora)
STRING	XP_006302805.1	1e-163	(Capsella rubella)

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
AT1G54830.3	1e-107	nuclear factor Y, subunit C3

Link Out ? help Back to Top
Phytozome	Carubv10020932m
Entrez Gene	17895105

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]