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

RrC1372_p3

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

MYB_related

Protein Properties

Length: 446aa MW: 50141.1 Da PI: 9.688

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1372_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	25.3	3.6e-08	133	174	4	46
S-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS Myb_DNA-binding 4 WTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 WT+eE ++l ++++++ + ++ Ia ++++ Rt +++k+r+++ RrC1372_p3 133 WTKEETDQLFELCERFDLR-FTVIADRFPLPRTVEELKDRYYT 174 *****************.*****99********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF16282	2.9E-30	105	179	IPR032563	DAMP1, SANT/Myb-like domain
SuperFamily	SSF46689	5.06E-7	129	183	IPR009057	Homeodomain-like
SMART	SM00717	3.0E-9	129	178	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	7.5E-7	132	177	IPR009057	Homeodomain-like
CDD	cd11658	3.86E-17	133	175	No hit	No description
Pfam	PF05499	2.2E-7	321	389	IPR008468	DNA methyltransferase 1-associated 1

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:0000812	Cellular Component	Swr1 complex
GO:0035267	Cellular Component	NuA4 histone acetyltransferase complex
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 446 aa Download sequence Send to blast
MGGTDAKDIL GLPKTPLSLS HEKKSRPQKE SHRKPDGISR EVYALTGGVA PLMPSIDVTH 60 LKRPPPPDEK VAWQWLPIKS SARKDDLQLF HWVRVVNSVP PTGDYSFAKY NKSVDILKYT 120 DDEYENHLTD PLWTKEETDQ LFELCERFDL RFTVIADRFP LPRTVEELKD RYYTVTRALL 180 RARAQSPSEL ANHPLMKEPY DITRDRERKR ALSMVLSQSR HQEKKDAEIL AEAKRITEMR 240 LAARRAADLD VSGNENVGLD KADGGPGCSV SPSSNSQLPA TAVAPSTLTM ADYTSTLASL 300 RMLHVYLRTY GLEQMVQAAS SAVGLRTIKR VEQTLQDLGV NLKPKVPTKT VCDEHLELRK 360 EILTLLNLQK QLQYKESEGS SHREGTYAAM PDTPKDRVFA SEPFSFGGVS ADRPIKKEPK 420 RKGPGRQADT PSPAHKRPRK LKASDL

Sequence ? help Back to Top

Protein Sequence Length: 446 aa Download sequence Send to blast

MGGTDAKDIL GLPKTPLSLS HEKKSRPQKE SHRKPDGISR EVYALTGGVA PLMPSIDVTH  60
LKRPPPPDEK VAWQWLPIKS SARKDDLQLF HWVRVVNSVP PTGDYSFAKY NKSVDILKYT  120
DDEYENHLTD PLWTKEETDQ LFELCERFDL RFTVIADRFP LPRTVEELKD RYYTVTRALL  180
RARAQSPSEL ANHPLMKEPY DITRDRERKR ALSMVLSQSR HQEKKDAEIL AEAKRITEMR  240
LAARRAADLD VSGNENVGLD KADGGPGCSV SPSSNSQLPA TAVAPSTLTM ADYTSTLASL  300
RMLHVYLRTY GLEQMVQAAS SAVGLRTIKR VEQTLQDLGV NLKPKVPTKT VCDEHLELRK  360
EILTLLNLQK QLQYKESEGS SHREGTYAAM PDTPKDRVFA SEPFSFGGVS ADRPIKKEPK  420
RKGPGRQADT PSPAHKRPRK LKASDL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3hm5_A	8e-19	104	184	4	88	DNA methyltransferase 1-associated protein 1
4iej_A	8e-19	104	184	4	88	DNA methyltransferase 1-associated protein 1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. {ECO:0000305\|Ref.5}.

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	AK353019	0.0	AK353019.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-19-J15.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018485149.1	0.0	PREDICTED: SWR1-complex protein 4-like
Swissprot	Q8VZL6	0.0	SWC4_ARATH; SWR1-complex protein 4
TrEMBL	A0A397ZY08	0.0	A0A397ZY08_BRACM; Uncharacterized protein
STRING	Bo00954s060.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8543	24	35

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G47210.1	0.0	MYB_related family protein

Publications ? help Back to Top
Gómez-Zambrano Á, et al. Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes. Mol Plant, 2018. 11(6): p. 815-832 [PMID:29604400]