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_009134191.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 341aa MW: 39054.5 Da PI: 7.4176

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009134191.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	172.1	1.7e-53	9	138	1	129
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvka...eekewyfFskrdkkyatgkrknratksgyWkatgkdkev 92 +ppGfrFhPtdeel+++yLkkk++ +k+e+ evi+evd++k+ePwdL++++k +kewyfFs++d+ky+tg+r+nrat++g+Wkatg+dk + XP_009134191.1 9 VPPGFRFHPTDEELLHYYLKKKISYHKFEM-EVIREVDLNKLEPWDLQERCKIgstPQKEWYFFSHKDRKYPTGSRTNRATHAGFWKATGRDKCI 102 69**************************.99**********964444223556********************************** PP NAM 93 lskkgelvglkktLvfykgrapkgektdWvmheyrle 129 + + +++g++ktLvfykgrap+g+ktdW+mheyrle XP_009134191.1 103 RN-SYKKIGMRKTLVFYKGRAPHGQKTDWIMHEYRLE 138 9.8999***************************85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	3.4E-60	8	160	IPR003441	NAC domain
PROSITE profile	PS51005	58.126	9	160	IPR003441	NAC domain
Pfam	PF02365	9.9E-28	10	137	IPR003441	NAC domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009834	Biological Process	plant-type secondary cell wall biogenesis
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0048829	Biological Process	root cap development
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 341 aa Download sequence Send to blast
MGSSSNGGVP PGFRFHPTDE ELLHYYLKKK ISYHKFEMEV IREVDLNKLE PWDLQERCKI 60 GSTPQKEWYF FSHKDRKYPT GSRTNRATHA GFWKATGRDK CIRNSYKKIG MRKTLVFYKG 120 RAPHGQKTDW IMHEYRLEDT DDPQGNPSED GWVVCRVFMK KNLFKVVTEG GSSINSTDQY 180 NHDASNNNNS LQARSFMHRD SPYQLVRNHG ATTLELNKPD LTLHQYPPIF HKPPSLGFDY 240 SAGLPRDCES AASEGLQYQQ ACEPGLEVGT CETVASHNHQ QGLGEWSMMD RLVTCHMGNE 300 DSSRGIRFED GNNNSSSVVQ PVPETNQLSL RSEMDFWGYS K

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	1e-52	9	162	17	167	NO APICAL MERISTEM PROTEIN
1ut4_B	1e-52	9	162	17	167	NO APICAL MERISTEM PROTEIN
1ut7_A	1e-52	9	162	17	167	NO APICAL MERISTEM PROTEIN
1ut7_B	1e-52	9	162	17	167	NO APICAL MERISTEM PROTEIN
3swm_A	1e-52	9	162	20	170	NAC domain-containing protein 19
3swm_B	1e-52	9	162	20	170	NAC domain-containing protein 19
3swm_C	1e-52	9	162	20	170	NAC domain-containing protein 19
3swm_D	1e-52	9	162	20	170	NAC domain-containing protein 19
3swp_A	1e-52	9	162	20	170	NAC domain-containing protein 19
3swp_B	1e-52	9	162	20	170	NAC domain-containing protein 19
3swp_C	1e-52	9	162	20	170	NAC domain-containing protein 19
3swp_D	1e-52	9	162	20	170	NAC domain-containing protein 19
4dul_A	1e-52	9	162	17	167	NAC domain-containing protein 19
4dul_B	1e-52	9	162	17	167	NAC domain-containing protein 19
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detectable in lateral root development when they reach 10 mm long. {ECO:0000269\|PubMed:20197506}.
Uniprot	TISSUE SPECIFICITY: Expressed throughout the root cap, in both columella (COL) and lateral root cap (LRC) cells, with higher levels in the COL-adjoining LRC than the upper LRC. Also present at low levels expression in the tips of cotyledons and the cotyledon vasculature, as weel as in vasculature of the first pair of true leaves and at the hydathodes. {ECO:0000269\|PubMed:20197506}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator. Together with BRN1 and SMB, regulates cellular maturation of root cap. Promotes the expression of genes involved in secondary cell walls (SCW) biosynthesis. {ECO:0000269\|PubMed:20197506}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00431	DAP	Transfer from AT4G10350	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009134191.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY133681	0.0	AY133681.1 Arabidopsis thaliana clone C103095 putative NAM/NAP (At4g10350) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009134191.1	0.0	PREDICTED: protein BEARSKIN2
Swissprot	Q9SV87	0.0	BRN2_ARATH; Protein BEARSKIN2
TrEMBL	A0A3P5ZJW6	0.0	A0A3P5ZJW6_BRACM; Uncharacterized protein
TrEMBL	M4C931	0.0	M4C931_BRARP; Uncharacterized protein
STRING	Bra000709.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5213	26	48

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G10350.1	0.0	NAC domain containing protein 70

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] Kamiya M, et al. Control of root cap maturation and cell detachment by BEARSKIN transcription factors in Arabidopsis. Development, 2016. 143(21): p. 4063-4072 [PMID:27803060]