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

Sopim05g055480.0.1

Organism

Solanum pimpinellifolium

Taxonomic ID

4084

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

NAC

Protein Properties

Length: 387aa MW: 43469 Da PI: 5.2676

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopim05g055480.0.1	genome	CSHL	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	166.4	9.6e-52	17	144	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLp..kkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkd 89 l+pGfrFhPtdeelv +yL++kv gk++++ ++++e+d+yk+eP dL ++vk+++ ewyfFs+ dkky +g+r nrat +gyWkatgkd Sopim05g055480.0.1 17 LAPGFRFHPTDEELVRYYLRRKVCGKPFRF-QAVTEIDVYKSEPCDLAgySSVKSRDMEWYFFSPVDKKYCNGSRLNRATGQGYWKATGKD 106 579***********************99.88**********85448888999***************************** PP NAM 90 kevlskkgelvglkktLvfykgrapkgektdWvmheyrl 128 +++ + k++++g+kktLvf++grap+g++t+Wvmheyrl Sopim05g055480.0.1 107 RHISH-KSQAIGMKKTLVFHSGRAPDGKRTNWVMHEYRL 144 9.999**************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	1.7E-60	11	167	IPR003441	NAC domain
PROSITE profile	PS51005	56.416	17	167	IPR003441	NAC domain
Pfam	PF02365	2.0E-28	19	144	IPR003441	NAC domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009555	Biological Process	pollen development
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0005730	Cellular Component	nucleolus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 387 aa Download sequence Send to blast
MEQEGSKGAV TVAPTSLAPG FRFHPTDEEL VRYYLRRKVC GKPFRFQAVT EIDVYKSEPC 60 DLAGYSSVKS RDMEWYFFSP VDKKYCNGSR LNRATGQGYW KATGKDRHIS HKSQAIGMKK 120 TLVFHSGRAP DGKRTNWVMH EYRLADKELE KAGIVQDSFV LCRIFQKSGL GPPTGDRYAP 180 FIEEEWDDDS AVLPGGETED DAVNGVDARV ESNDLDQDAP PKIACDNENV IELRSLPFAC 240 KRERSEEPEL LSLSQNKKPK HDVPSSSRAN GSEDSTITSK DPENMMTTKD YPLALLGFPL 300 LESFEPKDPQ PSNPLTFDSS NLEKSVPPGY LKFISNLETE ILNVSMERET LKIEVMRAQA 360 MINVLQSRID LLTKENEDMR KLVRGG*

Sequence ? help Back to Top

Protein Sequence Length: 387 aa Download sequence Send to blast

MEQEGSKGAV TVAPTSLAPG FRFHPTDEEL VRYYLRRKVC GKPFRFQAVT EIDVYKSEPC  60
DLAGYSSVKS RDMEWYFFSP VDKKYCNGSR LNRATGQGYW KATGKDRHIS HKSQAIGMKK  120
TLVFHSGRAP DGKRTNWVMH EYRLADKELE KAGIVQDSFV LCRIFQKSGL GPPTGDRYAP  180
FIEEEWDDDS AVLPGGETED DAVNGVDARV ESNDLDQDAP PKIACDNENV IELRSLPFAC  240
KRERSEEPEL LSLSQNKKPK HDVPSSSRAN GSEDSTITSK DPENMMTTKD YPLALLGFPL  300
LESFEPKDPQ PSNPLTFDSS NLEKSVPPGY LKFISNLETE ILNVSMERET LKIEVMRAQA  360
MINVLQSRID LLTKENEDMR KLVRGG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	5e-50	16	167	16	165	NO APICAL MERISTEM PROTEIN
1ut4_B	5e-50	16	167	16	165	NO APICAL MERISTEM PROTEIN
1ut7_A	5e-50	16	167	16	165	NO APICAL MERISTEM PROTEIN
1ut7_B	5e-50	16	167	16	165	NO APICAL MERISTEM PROTEIN
3swm_A	5e-50	16	167	19	168	NAC domain-containing protein 19
3swm_B	5e-50	16	167	19	168	NAC domain-containing protein 19
3swm_C	5e-50	16	167	19	168	NAC domain-containing protein 19
3swm_D	5e-50	16	167	19	168	NAC domain-containing protein 19
3swp_A	5e-50	16	167	19	168	NAC domain-containing protein 19
3swp_B	5e-50	16	167	19	168	NAC domain-containing protein 19
3swp_C	5e-50	16	167	19	168	NAC domain-containing protein 19
3swp_D	5e-50	16	167	19	168	NAC domain-containing protein 19
4dul_A	5e-50	16	167	16	165	NAC domain-containing protein 19
4dul_B	5e-50	16	167	16	165	NAC domain-containing protein 19
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional repressor that binds to the motif 5'-(C/T)A(C/A)G-3' in the promoter of target genes (PubMed:25578968). Binds also to the 5'-CTTGNNNNNCAAG-3' consensus sequence in chromatin (PubMed:26617990). Can bind to the mitochondrial dysfunction motif (MDM) present in the upstream regions of mitochondrial dysfunction stimulon (MDS) genes involved in mitochondrial retrograde regulation (MRR) (PubMed:24045019). Together with NAC050 and JMJ14, regulates gene expression and flowering time by associating with the histone demethylase JMJ14, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968, PubMed:26617990). Regulates siRNA-dependent post-transcriptional gene silencing (PTGS) through SGS3 expression modulation (PubMed:28207953). Required during pollen development (PubMed:19237690). {ECO:0000269\|PubMed:19237690, ECO:0000269\|PubMed:24045019, ECO:0000269\|PubMed:25578968, ECO:0000269\|PubMed:26617990, ECO:0000269\|PubMed:28207953}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00612	ChIP-seq	Transfer from AT3G10490	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by type III effector proteins (TTEs) secreted by the pathogenic bacteria P.syringae pv. tomato DC3000 during basal defense. {ECO:0000269\|PubMed:16553893}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT014626	0.0	BT014626.1 Lycopersicon esculentum clone 134129R, mRNA sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004239709.1	0.0	NAC domain containing protein 50
Swissprot	Q9SQY0	1e-105	NAC52_ARATH; NAC domain containing protein 52
TrEMBL	A0A0V0I4D1	0.0	A0A0V0I4D1_SOLCH; Putative NAC domain-containing protein 78-like
STRING	Solyc05g055480.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA3140	24	48

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G10490.1	2e-95	NAC domain containing protein 52

Publications ? help Back to Top
Higgins JD,Ferdous M,Osman K,Franklin FC The RecQ helicase AtRECQ4A is required to remove inter-chromosomal telomeric connections that arise during meiotic recombination in Arabidopsis. Plant J., 2011. 65(3): p. 492-502 [PMID:21265901] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Zhang S, et al. C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. Cell Discov, 2019. [PMID:26617990] Butel N,Le Masson I,Bouteiller N,Vaucheret H,Elmayan T sgs1: a neomorphic nac52 allele impairing post-transcriptional gene silencing through SGS3 downregulation. Plant J., 2017. 90(3): p. 505-519 [PMID:28207953] Elmayan T, et al. Arabidopsis mutants impaired in cosuppression. Plant Cell, 1998. 10(10): p. 1747-58 [PMID:9761800]