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

Carubv10028272m

Common Name

CARUB_v10028272mg

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: 259aa MW: 27679 Da PI: 4.7457

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10028272m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	178.4	6.8e-56	60	164	1	102
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdf 91 ql++fw++q ie+++dfknh+lPlarikki+kadedv+misaeaP+l++kacelfilelt+rswlhaeenkrrtl+k+diaaa+trtdifdf Carubv10028272m 60 QLQMFWTYQrqeIEQVNDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDF 153 89***998899***************************************************************************** PP NF-YC 92 lvdivprdelk 102 lvdivpr+e+k Carubv10028272m 154 LVDIVPREEIK 164 *****9975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	9.72E-34	48	154	IPR009072	Histone-fold
Pfam	PF00808	1.9E-20	82	145	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
Gene3D	G3DSA:1.10.20.10	8.4E-37	83	160	IPR009072	Histone-fold

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: 259 aa Download sequence Send to blast
MDNNNNNNNN QPPPPTSVYP PNSAVTTVIP PPPPGSTSII AGGGGGGATY HHLLQQQQQQ 60 LQMFWTYQRQ EIEQVNDFKN HQLPLARIKK IMKADEDVRM ISAEAPILFA KACELFILEL 120 TIRSWLHAEE NKRRTLQKND IAAAITRTDI FDFLVDIVPR EEIKEEEDAA AAAAALGGGG 180 MVPQAASGVP YYYPPMGQPA VPGGMMIGRP AMDPSGVYAQ PPSQAWQSVW QNSAGGGGDD 240 VSYGSGGSSG HGNLDSQG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	5e-55	68	160	3	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	132	138	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). Involved in the abscisic acid (ABA) signaling pathway. {ECO:0000250, ECO:0000269\|PubMed:17322342}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10028272m

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	AB007649	0.0	AB007649.1 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MLE2.
GenBank	AK317038	0.0	AK317038.1 Arabidopsis thaliana AT5G63470 mRNA, complete cds, clone: RAFL19-94-G17.
GenBank	CP002688	0.0	CP002688.1 Arabidopsis thaliana chromosome 5 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006282031.1	0.0	nuclear transcription factor Y subunit C-4 isoform X2
Refseq	XP_023635978.1	0.0	nuclear transcription factor Y subunit C-4 isoform X1
Swissprot	Q9FMV5	1e-144	NFYC4_ARATH; Nuclear transcription factor Y subunit C-4
TrEMBL	R0GDZ3	0.0	R0GDZ3_9BRAS; Uncharacterized protein
STRING	XP_006282031.1	0.0	(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
AT5G63470.2	1e-114	nuclear factor Y, subunit C4

Link Out ? help Back to Top
Phytozome	Carubv10028272m
Entrez Gene	17875688

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] Qi M, et al. QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnol. J., 2019. 17(1): p. 252-263 [PMID:29878511]