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

mrna23561.1-v1.0-hybrid

Organism

Fragaria vesca

Taxonomic ID

57918

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria

Family

NAC

Protein Properties

Length: 696aa MW: 75677.3 Da PI: 6.2663

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
mrna23561.1-v1.0-hybrid	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	167.7	3.9e-52	24	151	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLp.k.kvkaeekewyfFskrdkkyatgkrknratksgyWk 84 l+pGfrFhPtdeelv +yLk+kv +k++++ ++i++vdiyk+ePwdL k ++k++++e+yfFs dkky +g r nrat+ gyWk mrna23561.1-v1.0-hybrid 24 LAPGFRFHPTDEELVIYYLKRKVCRKPFKF-NAISDVDIYKSEPWDLAcKsSLKSRDQEYYFFSALDKKYGNGARMNRATNMGYWK 108 579************************9.89**********85347788999************************ PP NAM 85 atgkdkevlskkgelvglkktLvfykgrapkgektdWvmheyrl 128 atg+d++v++ ++++vg+kktLvf++grap+g++t+Wvmheyrl mrna23561.1-v1.0-hybrid 109 ATGNDRPVKH-NNKTVGMKKTLVFHSGRAPDGKRTNWVMHEYRL 151 ******.999**************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	9.02E-59	21	176	IPR003441	NAC domain
PROSITE profile	PS51005	56.686	24	176	IPR003441	NAC domain
Pfam	PF02365	3.1E-26	26	151	IPR003441	NAC domain
Gene3D	G3DSA:2.150.10.10	1.7E-13	220	379	IPR011049	Serralysin-like metalloprotease, C-terminal
SuperFamily	SSF51120	1.22E-9	220	357	IPR011049	Serralysin-like metalloprotease, C-terminal

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: 696 aa Download sequence Send to blast
MGHELVPSTT TPPLAKPPAA PTALAPGFRF HPTDEELVIY YLKRKVCRKP FKFNAISDVD 60 IYKSEPWDLA CKSSLKSRDQ EYYFFSALDK KYGNGARMNR ATNMGYWKAT GNDRPVKHNN 120 KTVGMKKTLV FHSGRAPDGK RTNWVMHEYR LVDTEMERPG NGVPQDAYVL CRVFHKSNIG 180 PPNGHRYAPF VEEEWDDEKL TFVPGEVARD ETSAAHDSVG NHRDVVMLGN GHDFVGGNGH 240 DSVGGNHYNV VMVGNGHDSA VGGNHRDFIM VGNGHHSVVG GNHRDVVMAG NGHDSVVGGN 300 CRDVVVIGNG RDSVVGGPIP DAVVGANGCH ALVFGNGRDT VAGNARDAAV GGNGHAAAFI 360 EQDVHDAVDI DQKDHVSMVV EQKDNAFASI EQKDHNVCIG GNGHGPSVDG HVQNNKMEVD 420 GHGTTKEGNV HGSIGGNGLK GATAGNYIVQ ESGSAEVAIA QDLLILLAGQ KWYCRPWDTQ 480 TISNALLSAT ELPKEDPTVL VPCKSEKLDD DPVTCVINRE ERLDDYPSPL TDDPQPLLSL 540 FNQQPGILRQ YKRRRHNESN SNRSNASEIS SGMTHDPCSS TTTTASTEAS VTASTKRNFL 600 SALVEFQLLE SLEPKDKTPV APPEFNAALH NSSVPSSCLK FIESLQNEIH KISIEKETLK 660 FEMLSSQAVI NILQSRIDLL NKENEELKRN AREAE*

Sequence ? help Back to Top

Protein Sequence Length: 696 aa Download sequence Send to blast

MGHELVPSTT TPPLAKPPAA PTALAPGFRF HPTDEELVIY YLKRKVCRKP FKFNAISDVD  60
IYKSEPWDLA CKSSLKSRDQ EYYFFSALDK KYGNGARMNR ATNMGYWKAT GNDRPVKHNN  120
KTVGMKKTLV FHSGRAPDGK RTNWVMHEYR LVDTEMERPG NGVPQDAYVL CRVFHKSNIG  180
PPNGHRYAPF VEEEWDDEKL TFVPGEVARD ETSAAHDSVG NHRDVVMLGN GHDFVGGNGH  240
DSVGGNHYNV VMVGNGHDSA VGGNHRDFIM VGNGHHSVVG GNHRDVVMAG NGHDSVVGGN  300
CRDVVVIGNG RDSVVGGPIP DAVVGANGCH ALVFGNGRDT VAGNARDAAV GGNGHAAAFI  360
EQDVHDAVDI DQKDHVSMVV EQKDNAFASI EQKDHNVCIG GNGHGPSVDG HVQNNKMEVD  420
GHGTTKEGNV HGSIGGNGLK GATAGNYIVQ ESGSAEVAIA QDLLILLAGQ KWYCRPWDTQ  480
TISNALLSAT ELPKEDPTVL VPCKSEKLDD DPVTCVINRE ERLDDYPSPL TDDPQPLLSL  540
FNQQPGILRQ YKRRRHNESN SNRSNASEIS SGMTHDPCSS TTTTASTEAS VTASTKRNFL  600
SALVEFQLLE SLEPKDKTPV APPEFNAALH NSSVPSSCLK FIESLQNEIH KISIEKETLK  660
FEMLSSQAVI NILQSRIDLL NKENEELKRN AREAE*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3swm_A	2e-46	18	178	14	170	NAC domain-containing protein 19
3swm_B	2e-46	18	178	14	170	NAC domain-containing protein 19
3swm_C	2e-46	18	178	14	170	NAC domain-containing protein 19
3swm_D	2e-46	18	178	14	170	NAC domain-containing protein 19
3swp_A	2e-46	18	178	14	170	NAC domain-containing protein 19
3swp_B	2e-46	18	178	14	170	NAC domain-containing protein 19
3swp_C	2e-46	18	178	14	170	NAC domain-containing protein 19
3swp_D	2e-46	18	178	14	170	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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	mrna23561.1-v1.0-hybrid

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}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004307019.1	0.0	PREDICTED: uncharacterized protein LOC101300663
Swissprot	Q9SQY0	1e-97	NAC52_ARATH; NAC domain containing protein 52
TrEMBL	A0A2P6SCG4	0.0	A0A2P6SCG4_ROSCH; Putative transcription factor NAM family
STRING	XP_004307019.1	0.0	(Fragaria vesca)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF8189	32	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G10490.1	5e-94	NAC domain containing protein 52

Link Out ? help Back to Top
Phytozome	mrna23561.1-v1.0-hybrid

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]