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

RrC13830_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

NAC

Protein Properties

Length: 291aa MW: 33339 Da PI: 7.4207

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC13830_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	103.2	3.5e-32	19	93	53	128
NAM 53 aeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlskkgelvglkktLvfykgrapkgektdWvmheyrl 128 +e++ewyfFs++d+ky+tg+r+nrat++g+Wkatg+dk+vls k++++g++ktLv+ykgrap+g+k dW+mheyrl RrC13830_p1 19 EEQSEWYFFSHKDRKYPTGTRTNRATAAGFWKATGRDKAVLS-KNNVIGMRKTLVYYKGRAPNGRKLDWIMHEYRL 93 4677************************************.8899*************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51005	37.637	1	122	IPR003441	NAC domain
SuperFamily	SSF101941	5.23E-36	19	122	IPR003441	NAC domain
Pfam	PF02365	6.4E-15	23	93	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:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 291 aa Download sequence Send to blast
MTLINSWGCT AARCKLGYEE QSEWYFFSHK DRKYPTGTRT NRATAAGFWK ATGRDKAVLS 60 KNNVIGMRKT LVYYKGRAPN GRKLDWIMHE YRLQNSELAP VQKPILCAIQ EEGWVVCRAF 120 RKPIPNQRPL GYETWQNQLH HVDNSNNYSS SATMNTSHHI GASSSSQNFN QMVMSNNHYN 180 ANNPSSTMHQ YGNIELPQLD SPSLSPSLGT NKDHNESLEQ EEEKSFNYVD WRTLDSLLDI 240 QVTHPQNPNV LVSSLAMQSY NPEQSFPSMH QNYNYEVEAN IHHSLGFFPD S

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	2e-27	21	122	70	165	NO APICAL MERISTEM PROTEIN
1ut4_B	2e-27	21	122	70	165	NO APICAL MERISTEM PROTEIN
1ut7_A	2e-27	21	122	70	165	NO APICAL MERISTEM PROTEIN
1ut7_B	2e-27	21	122	70	165	NO APICAL MERISTEM PROTEIN
3swm_A	2e-27	21	122	73	168	NAC domain-containing protein 19
3swm_B	2e-27	21	122	73	168	NAC domain-containing protein 19
3swm_C	2e-27	21	122	73	168	NAC domain-containing protein 19
3swm_D	2e-27	21	122	73	168	NAC domain-containing protein 19
3swp_A	2e-27	21	122	73	168	NAC domain-containing protein 19
3swp_B	2e-27	21	122	73	168	NAC domain-containing protein 19
3swp_C	2e-27	21	122	73	168	NAC domain-containing protein 19
3swp_D	2e-27	21	122	73	168	NAC domain-containing protein 19
4dul_A	2e-27	21	122	70	165	NAC domain-containing protein 19
4dul_B	2e-27	21	122	70	165	NAC domain-containing protein 19
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that binds to the secondary wall NAC binding element (SNBE), 5'-(T/A)NN(C/T)(T/C/G)TNNNNNNNA(A/C)GN(A/C/T)(A/T)-3', in the promoter of target genes (e.g. genes involved in secondary wall biosynthesis, cell wall modification such as xylan accumulation, and programmed cell death) (PubMed:20935069, PubMed:20488898, PubMed:22037706, PubMed:21284754). Involved in xylem formation in roots and shoots, especially regulating protoxylem vessel differentiation by promoting immature xylem vessel-specific genes expression (PubMed:16103214, PubMed:18445131, PubMed:20488898, PubMed:21498679, PubMed:21284754). Can activate the expression of several genes including XCP1, MYB46, NAC010/SND3, MYB103, MYB58, MYB63, MYB83, KNAT7, ASL19 and ASL20 (PubMed:17890373, PubMed:19088331, PubMed:18952777, PubMed:19122102, PubMed:19808805, PubMed:20935069, PubMed:21284754). {ECO:0000269\|PubMed:16103214, ECO:0000269\|PubMed:17890373, ECO:0000269\|PubMed:18445131, ECO:0000269\|PubMed:18952777, ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:19122102, ECO:0000269\|PubMed:19808805, ECO:0000269\|PubMed:20488898, ECO:0000269\|PubMed:20935069, ECO:0000269\|PubMed:21284754, ECO:0000269\|PubMed:21498679, ECO:0000269\|PubMed:22037706}.; FUNCTION: Required for the soilborne fungal pathogen Verticillium longisporum-induced transdifferentiation of chloroplast-containing bundle sheath cells to functional xylem elements leading to stunted growth, vein clearing, and leaf chloroses, as well as xylem hyperplasia within the vasculature of leaves, hypocotyls, and roots due to reinitiation of cambial activity and transdifferentiation of xylem parenchyma cells. This developmental reprogramming mediates also an increased drought stress tolerance. {ECO:0000269\|PubMed:23023171}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By brassinosteroids (e.g. brassinolide BL), auxin (e.g. 2,4-dichlorphenoxyacetic acid 2,4-D) and cytokinin (e.g. kinetin), with a synergistic effect (PubMed:16103214, PubMed:22345435). Up-regulated in a feed-back loop by ASL20 (PubMed:19088331). Levels are monitored by proteasome-mediated degradation (PubMed:18445131). Repressed by WEE1 upon replication stress to prevent premature tracheary element differentiation (PubMed:21498679). Accumulates during infection by the soilborne fungal pathogen Verticillium longisporum, especially in tissues undergoing de novo xylem formation (PubMed:23023171). {ECO:0000269\|PubMed:16103214, ECO:0000269\|PubMed:18445131, ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:21498679, ECO:0000269\|PubMed:22345435, ECO:0000269\|PubMed:23023171}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018462524.1	0.0	PREDICTED: NAC domain-containing protein 30-like
Swissprot	Q9C8W9	1e-174	NAC30_ARATH; NAC domain-containing protein 30
TrEMBL	A0A3P6DKS2	0.0	A0A3P6DKS2_BRAOL; Uncharacterized protein
STRING	Bo2g075130.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6950	27	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G71930.1	1e-153	vascular related NAC-domain protein 7

Publications ? help Back to Top
Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Kakehi J, et al. Mutations in ribosomal proteins, RPL4 and RACK1, suppress the phenotype of a thermospermine-deficient mutant of Arabidopsis thaliana. PLoS ONE, 2015. 10(1): p. e0117309 [PMID:25625317] Li Z, et al. A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis. Plant Physiol., 2016. 172(2): p. 1334-1351 [PMID:27566165] de Lucas M, et al. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation. Plant Cell, 2016. 28(10): p. 2616-2631 [PMID:27650334] Tan TT, et al. Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation. Plant Physiol., 2018. 176(1): p. 773-789 [PMID:29133368] Ohashi-Ito K,Iwamoto K,Fukuda H LOB DOMAIN-CONTAINING PROTEIN 15 Positively Regulates Expression of VND7, a Master Regulator of Tracheary Elements. Plant Cell Physiol., 2018. 59(5): p. 989-996 [PMID:29444288]