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

Dca36884.1

Organism

Dianthus caryophyllus

Taxonomic ID

3570

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Caryophyllaceae; Caryophylleae; Dianthus

Family

HB-other

Protein Properties

Length: 236aa MW: 26947.9 Da PI: 5.0306

Description

HB-other family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Dca36884.1	genome	DCA	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	17.5	7.1e-06	15	71	6	50
S--HHHHHHHHHHHHH..SSS--HHHHHHHHHHC..........TS-HHHHHHHHHH CS Homeobox 6 tftkeqleeLeelFek..nrypsaeereeLAkkl..........gLterqVkvWFqN 50 f+++++ e+e+ F+ + +++e ++LA++ +Lt +qV+ WFq Dca36884.1 15 IFSPSEIAEMENIFRDigKDSLNQEFYQDLATSFsssncrvgkpSLTWEQVQSWFQD 71 69***********667************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50071	8.697	7	79	IPR001356	Homeobox domain
Pfam	PF16719	4.0E-40	105	232	IPR032001	SAWADEE domain
Pfam	PF15057	1.7E-6	110	233	IPR032770	Domain of unknown function DUF4537

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006306	Biological Process	DNA methylation
GO:0006346	Biological Process	methylation-dependent chromatin silencing
GO:0031047	Biological Process	gene silencing by RNA
GO:0003677	Molecular Function	DNA binding
GO:0003682	Molecular Function	chromatin binding

Sequence ? help Back to Top
Protein Sequence Length: 236 aa Download sequence Send to blast
MDVFSPDDSS QTSSIFSPSE IAEMENIFRD IGKDSLNQEF YQDLATSFSS SNCRVGKPSL 60 TWEQVQSWFQ DKLQGSQDSA DASCTRNTPQ TSIVLKGGTA AELQELAFEA RSSRDNAWYD 120 VATFLSYRVL STGEHEARVR FAGFGNSHDE WVNVRTGVRE RSVPLDPSEC HKVKVGDHVL 180 CFQERPDYAV YVDAHIMEIQ RRLHDIKGCR CIYVVRFDDD KTEEKVQLNK ICWRPK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4iup_A	3e-58	105	236	3	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iup_B	3e-58	105	236	3	134	SAWADEE HOMEODOMAIN HOMOLOG 1
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Functional Description ? help Back to Top
Source	Description
UniProt	Involved in RNA-directed DNA methylation (RdDM). Required for the silencing of some endogenous RdDM targets and accumulation of 24-nt siRNAs, but not for the production of Pol V-dependent transcripts. Functions in transcriptional silencing through both DNA methylation-dependent and -independent pathways. Required for both maintenance and de-novo DNA methylation. Plays a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM. {ECO:0000269\|PubMed:21811420, ECO:0000269\|PubMed:22064704, ECO:0000269\|PubMed:23636332, ECO:0000269\|PubMed:23637343}.

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_010690199.1	1e-130	PREDICTED: protein SAWADEE HOMEODOMAIN HOMOLOG 1
Swissprot	Q9XI47	1e-81	SHH1_ARATH; Protein SAWADEE HOMEODOMAIN HOMOLOG 1
TrEMBL	A0A0K9R232	1e-122	A0A0K9R232_SPIOL; Uncharacterized protein
STRING	XP_010690199.1	1e-129	(Beta vulgaris)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G18380.1	1e-51	sequence-specific DNA binding transcription factors;sequence-specific DNA binding

Publications ? help Back to Top
Liu J, et al. An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing. Cell Res., 2011. 21(12): p. 1691-700 [PMID:22064704] Law JA, et al. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature, 2013. 498(7454): p. 385-9 [PMID:23636332] Ma L, et al. Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway. Genome Biol Evol, 2015. 7(9): p. 2648-62 [PMID:26338185] Wang F,Axtell MJ AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana. Plant J., 2017. 90(1): p. 37-47 [PMID:28002617]