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

GSBRNA2T00106173001

Common Name

GSBRNA2T00106173001, GSBRNA2T00108261001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

NAC

Protein Properties

Length: 274aa MW: 30184.6 Da PI: 10.2034

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00106173001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	116.3	3e-36	28	115	42	128
NAM 42 vePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlsk.kgelvglkktLvfykgrapkgektdWvmheyrl 128 ++Pw+Lp+k+k +ekew+fF++rd+ky+tg r+nrat++gyWkatgkd+e++s+ +++l g+kktLvfykgrapkgek+ Wvmheyrl GSBRNA2T00106173001 28 SKPWELPEKAKMGEKEWHFFTRRDRKYPTGLRTNRATEAGYWKATGKDREIKSSkTNSLLGMKKTLVFYKGRAPKGEKSCWVMHEYRL 115 68***99999************************************9856677*************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51005	39.6	1	140	IPR003441	NAC domain
SuperFamily	SSF101941	6.28E-41	28	140	IPR003441	NAC domain
Pfam	PF02365	2.1E-16	30	115	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:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 274 aa Download sequence Send to blast
MKSSSLTSSL RKSLTPTSPV PPFLKLISKP WELPEKAKMG EKEWHFFTRR DRKYPTGLRT 60 NRATEAGYWK ATGKDREIKS SKTNSLLGMK KTLVFYKGRA PKGEKSCWVM HEYRLDGKFS 120 YHYITSSAKD EWVLSKVCLK SSVVSRETKL VSSSSVSVTS ISCSSSTGSL IAPVIDAFAT 180 EHVSCFSNTS ASHVDASFPI YLPAPPQSLP RQPRRIDDVA FGQFMGLGST GQFNIDAAFL 240 PNLPSLPPTF LHPPPQYYAP YGGAAVSSWP FAL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	3e-31	30	142	59	167	NO APICAL MERISTEM PROTEIN
1ut4_B	3e-31	30	142	59	167	NO APICAL MERISTEM PROTEIN
1ut7_A	3e-31	30	142	59	167	NO APICAL MERISTEM PROTEIN
1ut7_B	3e-31	30	142	59	167	NO APICAL MERISTEM PROTEIN
3swm_A	3e-31	30	142	62	170	NAC domain-containing protein 19
3swm_B	3e-31	30	142	62	170	NAC domain-containing protein 19
3swm_C	3e-31	30	142	62	170	NAC domain-containing protein 19
3swm_D	3e-31	30	142	62	170	NAC domain-containing protein 19
3swp_A	3e-31	30	142	62	170	NAC domain-containing protein 19
3swp_B	3e-31	30	142	62	170	NAC domain-containing protein 19
3swp_C	3e-31	30	142	62	170	NAC domain-containing protein 19
3swp_D	3e-31	30	142	62	170	NAC domain-containing protein 19
4dul_A	3e-31	30	142	59	167	NAC domain-containing protein 19
4dul_B	3e-31	30	142	59	167	NAC domain-containing protein 19
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.27620	1e-158	seed

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: First observed in young embryonic SAM. Later confined to the boundaries between cotyledon primordia and the SAM. In mature embryos, localized around first leaves primordia. Only weakly present in vegetative SAM. In inflorescence, observed at the boundaries between floral organ primordia. In callus, expressed during transition to shoot development, with a progressive restriction to specific areas corresponding to future shoot apex. {ECO:0000269\|PubMed:11245578, ECO:0000269\|PubMed:12492830}.
Uniprot	TISSUE SPECIFICITY: Expressed in inflorescence stems, rosette leaves, aerial parts of seedlings, flowers, floral buds and roots. {ECO:0000269\|PubMed:11245578}.

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	GSBRNA2T00106173001

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	JN169820	0.0	JN169820.1 Brassica napus isolate Bna1 CUC1-like gene, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013694953.1	0.0	LOW QUALITY PROTEIN: protein CUP-SHAPED COTYLEDON 1
Swissprot	Q9FRV4	1e-108	NAC54_ARATH; Protein CUP-SHAPED COTYLEDON 1
TrEMBL	A0A0D3CK00	0.0	A0A0D3CK00_BRAOL; Uncharacterized protein
STRING	Bo5g127410.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13481	15	28

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15170.1	4e-88	NAC family protein

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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] 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]