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

XP_013603036.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 317aa MW: 35849.2 Da PI: 8.7904

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013603036.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	177.8	3e-55	16	143	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlsk 95 lppGfrFhPtdeel+++yL +k+++++++ ++i++vd++k+ePw+Lp+k+k + kewyfFs rd+ky+tg r+nrat++gyWk+tgkdke+l++ XP_013603036.1 16 LPPGFRFHPTDEELISYYLVNKIADQNFTG-KAIADVDLNKSEPWELPEKAKMGGKEWYFFSLRDRKYPTGVRTNRATNTGYWKTTGKDKEILNS 109 79***********************999.88***********99999************************************98 PP NAM 96 .kgelvglkktLvfykgrapkgektdWvmheyrl 128 ++elvg+kktLvfy+grap+gekt+Wvmheyrl XP_013603036.1 110 tTSELVGMKKTLVFYRGRAPRGEKTSWVMHEYRL 143 78889*************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	4.84E-63	13	165	IPR003441	NAC domain
PROSITE profile	PS51005	60.899	16	165	IPR003441	NAC domain
Pfam	PF02365	6.8E-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: 317 aa Download sequence Send to blast
MEQGDHQQQK KEEEALPPGF RFHPTDEELI SYYLVNKIAD QNFTGKAIAD VDLNKSEPWE 60 LPEKAKMGGK EWYFFSLRDR KYPTGVRTNR ATNTGYWKTT GKDKEILNST TSELVGMKKT 120 LVFYRGRAPR GEKTSWVMHE YRLHSKSSYR TSKQDEWVVC RVLKKTEATK KYTSNCSSST 180 SHHHQSHTRA SILSTNNNNP NYSSDLLQLP AHLQPHTCLN FNQTLMANAV HLAELSRVFR 240 ASTSSTMDSA HQQLMSYNHM PVSGLNLNLS GGLVQPTPPA MSLEDVVAVS ASLSGQNGFG 300 NVEMSRCMDL DGYWPSY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	1e-57	15	171	16	171	NO APICAL MERISTEM PROTEIN
1ut4_B	1e-57	15	171	16	171	NO APICAL MERISTEM PROTEIN
1ut7_A	1e-57	15	171	16	171	NO APICAL MERISTEM PROTEIN
1ut7_B	1e-57	15	171	16	171	NO APICAL MERISTEM PROTEIN
3swm_A	9e-58	15	171	19	174	NAC domain-containing protein 19
3swm_B	9e-58	15	171	19	174	NAC domain-containing protein 19
3swm_C	9e-58	15	171	19	174	NAC domain-containing protein 19
3swm_D	9e-58	15	171	19	174	NAC domain-containing protein 19
3swp_A	9e-58	15	171	19	174	NAC domain-containing protein 19
3swp_B	9e-58	15	171	19	174	NAC domain-containing protein 19
3swp_C	9e-58	15	171	19	174	NAC domain-containing protein 19
3swp_D	9e-58	15	171	19	174	NAC domain-containing protein 19
4dul_A	1e-57	15	171	16	171	NAC domain-containing protein 19
4dul_B	1e-57	15	171	16	171	NAC domain-containing protein 19
Search in ModeBase

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	XP_013603036.1

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	AC006403	1e-153	AC006403.4 Arabidopsis thaliana chromosome 2 clone T28I24 map mi238, complete sequence.
GenBank	CP002685	1e-153	CP002685.1 Arabidopsis thaliana chromosome 2, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013603036.1	0.0	PREDICTED: protein CUP-SHAPED COTYLEDON 1-like
Refseq	XP_022564004.1	0.0	protein CUP-SHAPED COTYLEDON 1
Swissprot	Q9FRV4	1e-79	NAC54_ARATH; Protein CUP-SHAPED COTYLEDON 1
TrEMBL	A0A0D3DVN0	0.0	A0A0D3DVN0_BRAOL; Uncharacterized protein
STRING	Bo8g099810.1	0.0	(Brassica oleracea)

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	0.0	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]