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

Solyc04g015060.1.1

Common Name

LOC101256476

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

NF-YB

Protein Properties

Length: 238aa MW: 26414.2 Da PI: 5.8943

Description

NF-YB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc04g015060.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YB	169.3	4.4e-53	56	150	1	95
NF-YB 1 vreqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyr 91 vreqdrf+Pianv+rim+k+lP +akis+daket+qecvsefisfvt+ea+d+cqre+rkti+++d+lwa+++lGf+dy+epl+++l++yr Solyc04g015060.1.1 56 VREQDRFMPIANVIRIMRKTLPPHAKISDDAKETIQECVSEFISFVTGEANDRCQREQRKTITAEDVLWAMSKLGFDDYIEPLTMHLHRYR 146 69***************************************************************************************** PP NF-YB 92 eleg 95 e++g Solyc04g015060.1.1 147 ECDG 150 *986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.20.10	9.6E-50	51	155	IPR009072	Histone-fold
SuperFamily	SSF47113	6.52E-38	59	157	IPR009072	Histone-fold
Pfam	PF00808	1.7E-26	62	126	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
PRINTS	PR00615	1.5E-16	90	108	No hit	No description
PROSITE pattern	PS00685	0	93	109	IPR003956	Transcription factor, NFYB/HAP3, conserved site
PRINTS	PR00615	1.5E-16	109	127	No hit	No description
PRINTS	PR00615	1.5E-16	128	146	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 238 aa Download sequence Send to blast
MDLGGGNGSG GFHGYRRFPQ TTSADGIATL NQAIPTTNHL NDNNNASVPD DSECTVREQD 60 RFMPIANVIR IMRKTLPPHA KISDDAKETI QECVSEFISF VTGEANDRCQ REQRKTITAE 120 DVLWAMSKLG FDDYIEPLTM HLHRYRECDG GDRGSLRGEP LMLMKSRGAM VDPAASTSIG 180 NNMTHVNYPL PPNFTMTHHH HGYYTYAHMT NDNVATNSQA NLDEANNNVE SFGEHNK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_A	3e-60	52	147	2	97	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed primarily during seed development. {ECO:0000269\|PubMed:12509518}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots, flowers and developing siliques. Present in etiolated seedlings. {ECO:0000269\|PubMed:11250072, ECO:0000269\|PubMed:12509518, ECO:0000269\|PubMed:17322342}.

Functional Description ? help Back to Top
Source	Description
UniProt	Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. Plays a role in the regulation of the embryogenesis. Involved in the abscisic acid (ABA) signaling pathway. {ECO:0000269\|PubMed:12509518, ECO:0000269\|PubMed:17322342}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc04g015060.1.1

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_015073076.1	0.0	nuclear transcription factor Y subunit B-6-like
Swissprot	Q84W66	1e-66	NFYB6_ARATH; Nuclear transcription factor Y subunit B-6
TrEMBL	A0A3Q7GRZ3	1e-179	A0A3Q7GRZ3_SOLLC; Uncharacterized protein
STRING	Solyc04g015060.1.1	1e-180	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA111	24	356
Representative plant	OGRP168	17	170

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G47670.2	2e-65	nuclear factor Y, subunit B6

Link Out ? help Back to Top
Phytozome	Solyc04g015060.1.1
Entrez Gene	101256476

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] Jia H,McCarty DR,Suzuki M Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression. Plant Physiol., 2013. 163(3): p. 1293-305 [PMID:24043445] Kim HU, et al. Ectopic overexpression of castor bean LEAFY COTYLEDON2 (LEC2) in Arabidopsis triggers the expression of genes that encode regulators of seed maturation and oil body proteins in vegetative tissues. FEBS Open Bio, 2013. 4: p. 25-32 [PMID:24363987] 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] Li D, et al. MYB89 Transcription Factor Represses Seed Oil Accumulation. Plant Physiol., 2017. 173(2): p. 1211-1225 [PMID:27932421] Zhao H, et al. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. Front Plant Sci, 2016. 7: p. 2045 [PMID:28119722] Han JD, et al. Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program. Front Plant Sci, 2017. 8: p. 439 [PMID:28421087]