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

Rsa1.0_12052.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 202aa MW: 23293.1 Da PI: 10.0613

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_12052.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	179.2	1.1e-55	16	143	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkat 86 lppGfrFhPtdeel+++yL +k+++++++ ++i++vd++k+ePw+Lp+k+k + kewyfFs rd+ky+tg r+nrat++gyWk+t Rsa1.0_12052.1_g00001.1 16 LPPGFRFHPTDEELISYYLVNKIADQNFTG-KAIADVDLNKSEPWELPEKAKIGGKEWYFFSLRDRKYPTGVRTNRATNTGYWKTT 100 79***********************999.88***********99999***************************** PP NAM 87 gkdkevlsk.kgelvglkktLvfykgrapkgektdWvmheyrl 128 gkdke+l++ ++elvg+kktLvfy+grap+gekt+Wvmheyrl Rsa1.0_12052.1_g00001.1 101 GKDKEILNStTSELVGMKKTLVFYRGRAPRGEKTSWVMHEYRL 143 ***9878889*************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	1.96E-63	12	165	IPR003441	NAC domain
PROSITE profile	PS51005	60.845	16	165	IPR003441	NAC domain
Pfam	PF02365	2.0E-29	17	143	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: 202 aa Download sequence Send to blast
MEQGDHQQQK KEVEALPPGF RFHPTDEELI SYYLVNKIAD QNFTGKAIAD VDLNKSEPWE 60 LPEKAKIGGK EWYFFSLRDR KYPTGVRTNR ATNTGYWKTT GKDKEILNST TSELVGMKKT 120 LVFYRGRAPR GEKTSWVMHE YRLHSKSSYR TSKQDEWVVC RVLKKAEATK KYISNSSSSA 180 SHHLQSHARA SILSTNNNNP NY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	4e-59	15	171	16	171	NO APICAL MERISTEM PROTEIN
1ut4_B	4e-59	15	171	16	171	NO APICAL MERISTEM PROTEIN
1ut7_A	4e-59	15	171	16	171	NO APICAL MERISTEM PROTEIN
1ut7_B	4e-59	15	171	16	171	NO APICAL MERISTEM PROTEIN
3swm_A	4e-59	15	171	19	174	NAC domain-containing protein 19
3swm_B	4e-59	15	171	19	174	NAC domain-containing protein 19
3swm_C	4e-59	15	171	19	174	NAC domain-containing protein 19
3swm_D	4e-59	15	171	19	174	NAC domain-containing protein 19
3swp_A	4e-59	15	171	19	174	NAC domain-containing protein 19
3swp_B	4e-59	15	171	19	174	NAC domain-containing protein 19
3swp_C	4e-59	15	171	19	174	NAC domain-containing protein 19
3swp_D	4e-59	15	171	19	174	NAC domain-containing protein 19
4dul_A	4e-59	15	171	16	171	NAC domain-containing protein 19
4dul_B	4e-59	15	171	16	171	NAC domain-containing protein 19
Search in ModeBase

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. Seems to act as an inhibitor of cell division. {ECO:0000269\|PubMed:10079219, ECO:0000269\|PubMed:10750709, ECO:0000269\|PubMed:11245578, ECO:0000269\|PubMed:12163400, ECO:0000269\|PubMed:12492830, ECO:0000269\|PubMed:12610213, ECO:0000269\|PubMed:12787253, ECO:0000269\|PubMed:14617069, ECO:0000269\|PubMed:15202996, ECO:0000269\|PubMed:15294871, ECO:0000269\|PubMed:15500463, ECO:0000269\|PubMed:15723790, ECO:0000269\|PubMed:16798887, ECO:0000269\|PubMed:17122068, ECO:0000269\|PubMed:17287247, ECO:0000269\|PubMed:9212461}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_12052.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By BRM, at the chromatin level, and conferring a very specific spatial expression pattern. Directly induced by ESR2 in response to cytokinins. 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:17056621, 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	AK228141	1e-103	AK228141.1 Arabidopsis thaliana mRNA for no apical meristem (NAM) -like protein, partial cds, clone: RAFL14-61-A06.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018437172.1	1e-149	PREDICTED: protein CUP-SHAPED COTYLEDON 1-like
Swissprot	Q9FRV4	2e-79	NAC54_ARATH; Protein CUP-SHAPED COTYLEDON 1
TrEMBL	R0G1T7	1e-134	R0G1T7_9BRAS; Uncharacterized protein
STRING	XP_006296338.1	1e-135	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6851	28	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G24430.2	1e-131	NAC domain containing protein 38

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Shinohara N,Ohbayashi I,Sugiyama M Involvement of rRNA biosynthesis in the regulation of CUC1 gene expression and pre-meristematic cell mound formation during shoot regeneration. Front Plant Sci, 2014. 5: p. 159 [PMID:24808900] 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] 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] 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]