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

RrC19605_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: 300aa MW: 33515 Da PI: 7.8723

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC19605_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	176	1e-54	20	147	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlsk.kg 97 +ppGfrFhPtdeel+++yL kkv ++++++ +i++vd++k+ePw+Lp+k+k +ekewyfF+ rd+ky++g r+nrat++gyWkatgkd+e++s+ ++ RrC19605_p1 20 MPPGFRFHPTDEELITYYLLKKVLDSNFSC-AAISQVDLNKCEPWELPEKAKMGEKEWYFFTLRDRKYPRGLRTNRATEAGYWKATGKDREIKSSkTK 116 79**************************.88***********99999************************************98566 PP NAM 98 elvglkktLvfykgrapkgektdWvmheyrl 128 +l g+kktLvfykgrapkgek+ Wvmheyrl RrC19605_p1 117 SLLGMKKTLVFYKGRAPKGEKSCWVMHEYRL 147 77*************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	3.92E-61	17	172	IPR003441	NAC domain
PROSITE profile	PS51005	57.172	20	172	IPR003441	NAC domain
Pfam	PF02365	1.1E-28	21	147	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: 300 aa Download sequence Send to blast
MDIDVLNGWE RSRFEDGTVM PPGFRFHPTD EELITYYLLK KVLDSNFSCA AISQVDLNKC 60 EPWELPEKAK MGEKEWYFFT LRDRKYPRGL RTNRATEAGY WKATGKDREI KSSKTKSLLG 120 MKKTLVFYKG RAPKGEKSCW VMHEYRLDGK FSYHYITSSA KDEWVLSKVC LKSSVVNRET 180 KLISSSVTGV SGSSSAGSVI APVIDTFATE HVSCFSNTSS SASHADAIFP TYLPAPPPSP 240 PRQPRSIDDD VGFGQFMGPG SSEQLSDDDA AFLLNQPSLP PTVLPLPPPQ WYALYGGEPR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	3e-49	20	178	17	171	NO APICAL MERISTEM PROTEIN
1ut4_B	3e-49	20	178	17	171	NO APICAL MERISTEM PROTEIN
1ut7_A	3e-49	20	178	17	171	NO APICAL MERISTEM PROTEIN
1ut7_B	3e-49	20	178	17	171	NO APICAL MERISTEM PROTEIN
3swm_A	4e-49	20	178	20	174	NAC domain-containing protein 19
3swm_B	4e-49	20	178	20	174	NAC domain-containing protein 19
3swm_C	4e-49	20	178	20	174	NAC domain-containing protein 19
3swm_D	4e-49	20	178	20	174	NAC domain-containing protein 19
3swp_A	4e-49	20	178	20	174	NAC domain-containing protein 19
3swp_B	4e-49	20	178	20	174	NAC domain-containing protein 19
3swp_C	4e-49	20	178	20	174	NAC domain-containing protein 19
3swp_D	4e-49	20	178	20	174	NAC domain-containing protein 19
4dul_A	3e-49	20	178	17	171	NAC domain-containing protein 19
4dul_B	3e-49	20	178	17	171	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. 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}.

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018487533.1	0.0	PREDICTED: protein CUP-SHAPED COTYLEDON 1-like
Swissprot	Q9FRV4	1e-147	NAC54_ARATH; Protein CUP-SHAPED COTYLEDON 1
TrEMBL	A0A3N6QB85	1e-167	A0A3N6QB85_BRACR; Uncharacterized protein
STRING	XP_010502576.1	1e-167	(Camelina sativa)

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	1e-134	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] 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]