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

RrC4136_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: 338aa MW: 37490.9 Da PI: 9.2414

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4136_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	179	1.2e-55	17	145	1	129
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlsk.kge 98 lppGfrFhPtdeel+++yL +kv + ++ ++i+evd++k+ePw+Lp k+k +ekewyfFs rd+ky+tg r+nrat++gyWkatgkd+e++s+ +++ RrC4136_p1 17 LPPGFRFHPTDEELITHYLLRKVLDGCFSS-RAIAEVDLNKCEPWQLPGKAKMGEKEWYFFSLRDRKYPTGLRTNRATEAGYWKATGKDREIYSSkTSA 114 79***********************999.89***********99999************************************985677 PP NAM 99 lvglkktLvfykgrapkgektdWvmheyrle 129 lvg+kktLvfykgrapkgek++Wvmheyrle RrC4136_p1 115 LVGMKKTLVFYKGRAPKGEKSSWVMHEYRLE 145 8**************************85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	6.15E-63	4	177	IPR003441	NAC domain
PROSITE profile	PS51005	59.153	17	177	IPR003441	NAC domain
Pfam	PF02365	5.6E-29	18	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:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 338 aa Download sequence Send to blast
MDIPYYHYDH GGDSQYLPPG FRFHPTDEEL ITHYLLRKVL DGCFSSRAIA EVDLNKCEPW 60 QLPGKAKMGE KEWYFFSLRD RKYPTGLRTN RATEAGYWKA TGKDREIYSS KTSALVGMKK 120 TLVFYKGRAP KGEKSSWVMH EYRLEGKFSY HFISRSSKIN ARPKSNDEWV ISRVFKKTGL 180 ANTGASAGAS ISISSGTGSS KKTKIPSSIS TTYREQPSSP SSVSLPPLLD PTTTLGYTDS 240 SWSYDSRNTN TTVTNTAITE HVSCFSTAAT TTALGLDVNN FSHFPYFGSS SASTMTTSAN 300 LPSFHGGTGM NYWLQTTAEE NETKAGLLNG GLDCVWNY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	6e-53	17	182	17	170	NO APICAL MERISTEM PROTEIN
1ut4_B	6e-53	17	182	17	170	NO APICAL MERISTEM PROTEIN
1ut7_A	6e-53	17	182	17	170	NO APICAL MERISTEM PROTEIN
1ut7_B	6e-53	17	182	17	170	NO APICAL MERISTEM PROTEIN
3swm_A	6e-53	17	182	20	173	NAC domain-containing protein 19
3swm_B	6e-53	17	182	20	173	NAC domain-containing protein 19
3swm_C	6e-53	17	182	20	173	NAC domain-containing protein 19
3swm_D	6e-53	17	182	20	173	NAC domain-containing protein 19
3swp_A	6e-53	17	182	20	173	NAC domain-containing protein 19
3swp_B	6e-53	17	182	20	173	NAC domain-containing protein 19
3swp_C	6e-53	17	182	20	173	NAC domain-containing protein 19
3swp_D	6e-53	17	182	20	173	NAC domain-containing protein 19
4dul_A	6e-53	17	182	17	170	NAC domain-containing protein 19
4dul_B	6e-53	17	182	17	170	NAC domain-containing protein 19
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator of STM and KNAT6. Involved in molecular mechanisms regulating shoot apical meristem (SAM) formation during embryogenesis and organ separation. Required for the fusion of septa of gynoecia along the length of the ovaries. Activates the shoot formation in callus in a STM-dependent manner. Controls leaf margin development and required for leaf serration. Involved in axillary meristem initiation and separation of the meristem from the main stem. Regulates the phyllotaxy throughout the plant development. Seems to act as an inhibitor of cell division. {ECO:0000269\|PubMed:10079219, ECO:0000269\|PubMed:10750709, ECO:0000269\|PubMed:12163400, ECO:0000269\|PubMed:12492830, ECO:0000269\|PubMed:12610213, ECO:0000269\|PubMed:15202996, ECO:0000269\|PubMed:15294871, ECO:0000269\|PubMed:15500463, ECO:0000269\|PubMed:15723790, ECO:0000269\|PubMed:16798887, ECO:0000269\|PubMed:17098808, ECO:0000269\|PubMed:17122068, ECO:0000269\|PubMed:17251269, ECO:0000269\|PubMed:17287247, ECO:0000269\|PubMed:9212461}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By BRM and SYD, at the chromatin level, and conferring a very specific spatial expression pattern. Precise spatial regulation by post-transcriptional repression directed by the microRNA miR164. {ECO:0000269\|PubMed:15202996, ECO:0000269\|PubMed:15294871, ECO:0000269\|PubMed:15723790, ECO:0000269\|PubMed:16854978, ECO:0000269\|PubMed:17251269, ECO:0000269\|PubMed:17287247}.

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	BT030026	0.0	BT030026.1 Arabidopsis thaliana At5g53950 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009127127.1	0.0	PREDICTED: protein CUP-SHAPED COTYLEDON 2
Swissprot	O04017	0.0	NAC98_ARATH; Protein CUP-SHAPED COTYLEDON 2
TrEMBL	A0A3P6DH15	0.0	A0A3P6DH15_BRAOL; Uncharacterized protein
STRING	Bra022685.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6615	27	45

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G53950.1	1e-160	NAC family protein

Publications ? help Back to Top
Wang YX Characterization of a novel Medicago sativa NAC transcription factor gene involved in response to drought stress. Mol. Biol. Rep., 2013. 40(11): p. 6451-8 [PMID:24057250] Kamiuchi Y,Yamamoto K,Furutani M,Tasaka M,Aida M The CUC1 and CUC2 genes promote carpel margin meristem formation during Arabidopsis gynoecium development. Front Plant Sci, 2014. 5: p. 165 [PMID:24817871] Gonçalves B, et al. A conserved role for CUP-SHAPED COTYLEDON genes during ovule development. Plant J., 2015. 83(4): p. 732-42 [PMID:26119568] Du Q,Wang H The role of HD-ZIP III transcription factors and miR165/166 in vascular development and secondary cell wall formation. Plant Signal Behav, 2015. 10(10): p. e1078955 [PMID:26340415] Vialette-Guiraud AC, et al. A Conserved Role for the NAM/miR164 Developmental Module Reveals a Common Mechanism Underlying Carpel Margin Fusion in Monocarpous and Syncarpous Eurosids. Front Plant Sci, 2015. 6: p. 1239 [PMID:26793217] Cui X, et al. REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nat. Genet., 2016. 48(6): p. 694-9 [PMID:27111035] Blein T,Pautot V,Laufs P Combinations of Mutations Sufficient to Alter Arabidopsis Leaf Dissection. Plants (Basel), 2013. 2(2): p. 230-47 [PMID:27137374] Biot E, et al. Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis. Development, 2016. 143(18): p. 3417-28 [PMID:27387872] Zheng M, et al. Chloroplast Translation Initiation Factors Regulate Leaf Variegation and Development. Plant Physiol., 2016. 172(2): p. 1117-1130 [PMID:27535792] Balkunde R,Kitagawa M,Xu XM,Wang J,Jackson D SHOOT MERISTEMLESS trafficking controls axillary meristem formation, meristem size and organ boundaries in Arabidopsis. Plant J., 2017. 90(3): p. 435-446 [PMID:28161901] Koyama T,Sato F,Ohme-Takagi M Roles of miR319 and TCP Transcription Factors in Leaf Development. Plant Physiol., 2017. 175(2): p. 874-885 [PMID:28842549] González-Carranza ZH, et al. HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS ONE, 2017. 12(9): p. e0185106 [PMID:28934292] Wilson-Sánchez D,Martínez-López S,Navarro-Cartagena S,Jover-Gil S,Micol JL Members of the DEAL subfamily of the DUF1218 gene family are required for bilateral symmetry but not for dorsoventrality in Arabidopsis leaves. New Phytol., 2018. 217(3): p. 1307-1321 [PMID:29139551] Gonçalves B, et al. GDP-L-fucose is required for boundary definition in plants. J. Exp. Bot., 2017. 68(21-22): p. 5801-5811 [PMID:29186469] Sha S, et al. To be serrate or pinnate: diverse leaf forms of yarrows (Achillea) are linked to differential expression patterns of NAM genes. Ann. Bot., 2018. 121(2): p. 255-266 [PMID:29267935] Maugarny-Calès A, et al. Dissecting the pathways coordinating patterning and growth by plant boundary domains. PLoS Genet., 2019. 15(1): p. e1007913 [PMID:30677017]