AT5G39550 (VIM3, ORTH1)

Aliases : VIM3, ORTH1

Description : Zinc finger (C3HC4-type RING finger) family protein

Gene families : OG0002340 (Archaeplastida) Phylogenetic Tree(s): OG0002340_tree ,
OG_05_0002708 (LandPlants) Phylogenetic Tree(s): OG_05_0002708_tree ,
OG_06_0002795 (SeedPlants) Phylogenetic Tree(s): OG_06_0002795_tree

Sequence : coding (download), protein (download)

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Note:Only the main profile, including all conditions, is shown. Additional statistics and tissue specific profiles are available here.

Type	Description	Actions
Neighborhood	HRR: AT5G39550
Cluster	HCCA: Cluster_24

Target	Alias	Description	ECC score	Gene Family Method	Actions
AT1G66050	VIM2, ORTH5	Zinc finger (C3HC4-type RING finger) family protein	0.04	Archaeplastida

Type	GO Term	Name	Evidence	Source
MF	GO:0000166	nucleotide binding	None	Extended
BP	GO:0003006	developmental process involved in reproduction	None	Extended
MF	GO:0003674	molecular_function	None	Extended
MF	GO:0003676	nucleic acid binding	None	Extended
MF	GO:0003677	DNA binding	None	Extended
MF	GO:0003824	catalytic activity	None	Extended
MF	GO:0004842	ubiquitin-protein transferase activity	IDA	Interproscan
MF	GO:0005488	binding	None	Extended
CC	GO:0005575	cellular_component	None	Extended
CC	GO:0005634	nucleus	IDA	Interproscan
CC	GO:0005634	nucleus	ISM	Interproscan
BP	GO:0006139	nucleobase-containing compound metabolic process	None	Extended
BP	GO:0006259	DNA metabolic process	None	Extended
BP	GO:0006304	DNA modification	None	Extended
BP	GO:0006305	DNA alkylation	None	Extended
BP	GO:0006306	DNA methylation	None	Extended
BP	GO:0006355	regulation of transcription, DNA-templated	None	Extended
BP	GO:0006464	cellular protein modification process	None	Extended
BP	GO:0006725	cellular aromatic compound metabolic process	None	Extended
BP	GO:0006807	nitrogen compound metabolic process	None	Extended
BP	GO:0008150	biological_process	None	Extended
BP	GO:0008152	metabolic process	None	Extended
MF	GO:0008270	zinc ion binding	ISS	Interproscan
MF	GO:0008327	methyl-CpG binding	IDA	Interproscan
BP	GO:0009889	regulation of biosynthetic process	None	Extended
BP	GO:0009893	positive regulation of metabolic process	None	Extended
BP	GO:0009987	cellular process	None	Extended
BP	GO:0010228	vegetative to reproductive phase transition of meristem	IMP	Interproscan
BP	GO:0010424	DNA methylation on cytosine within a CG sequence	IMP	Interproscan
MF	GO:0010428	methyl-CpNpG binding	IDA	Interproscan
MF	GO:0010429	methyl-CpNpN binding	IDA	Interproscan
BP	GO:0010468	regulation of gene expression	None	Extended
BP	GO:0010556	regulation of macromolecule biosynthetic process	None	Extended
BP	GO:0010604	positive regulation of macromolecule metabolic process	None	Extended
BP	GO:0010638	positive regulation of organelle organization	None	Extended
BP	GO:0016567	protein ubiquitination	IDA	Interproscan
MF	GO:0016740	transferase activity	None	Extended
BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	None	Extended
BP	GO:0019222	regulation of metabolic process	None	Extended
BP	GO:0019538	protein metabolic process	None	Extended
MF	GO:0019787	ubiquitin-like protein transferase activity	None	Extended
BP	GO:0022414	reproductive process	None	Extended
BP	GO:0031323	regulation of cellular metabolic process	None	Extended
BP	GO:0031325	positive regulation of cellular metabolic process	None	Extended
BP	GO:0031326	regulation of cellular biosynthetic process	None	Extended
BP	GO:0031935	regulation of chromatin silencing	None	Extended
BP	GO:0031937	positive regulation of chromatin silencing	None	Extended
BP	GO:0032259	methylation	None	Extended
BP	GO:0032446	protein modification by small protein conjugation	None	Extended
BP	GO:0032502	developmental process	None	Extended
BP	GO:0032776	DNA methylation on cytosine	IMP	Interproscan
BP	GO:0033043	regulation of organelle organization	None	Extended
BP	GO:0033044	regulation of chromosome organization	None	Extended
BP	GO:0034641	cellular nitrogen compound metabolic process	None	Extended
MF	GO:0036094	small molecule binding	None	Extended
BP	GO:0036211	protein modification process	None	Extended
MF	GO:0043167	ion binding	None	Extended
MF	GO:0043169	cation binding	None	Extended
BP	GO:0043170	macromolecule metabolic process	None	Extended
CC	GO:0043226	organelle	None	Extended
CC	GO:0043227	membrane-bounded organelle	None	Extended
CC	GO:0043229	intracellular organelle	None	Extended
CC	GO:0043231	intracellular membrane-bounded organelle	None	Extended
BP	GO:0043412	macromolecule modification	None	Extended
BP	GO:0043414	macromolecule methylation	None	Extended
MF	GO:0043565	sequence-specific DNA binding	None	Extended
BP	GO:0044237	cellular metabolic process	None	Extended
BP	GO:0044238	primary metabolic process	None	Extended
BP	GO:0044260	cellular macromolecule metabolic process	None	Extended
BP	GO:0044267	cellular protein metabolic process	None	Extended
CC	GO:0044424	intracellular part	None	Extended
CC	GO:0044464	cell part	None	Extended
BP	GO:0044728	DNA methylation or demethylation	None	Extended
BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	None	Extended
BP	GO:0046483	heterocycle metabolic process	None	Extended
MF	GO:0046872	metal ion binding	None	Extended
MF	GO:0046914	transition metal ion binding	None	Extended
BP	GO:0048518	positive regulation of biological process	None	Extended
BP	GO:0048522	positive regulation of cellular process	None	Extended
BP	GO:0050789	regulation of biological process	None	Extended
BP	GO:0050794	regulation of cellular process	None	Extended
BP	GO:0051052	regulation of DNA metabolic process	None	Extended
BP	GO:0051054	positive regulation of DNA metabolic process	None	Extended
BP	GO:0051128	regulation of cellular component organization	None	Extended
BP	GO:0051130	positive regulation of cellular component organization	None	Extended
BP	GO:0051171	regulation of nitrogen compound metabolic process	None	Extended
BP	GO:0051173	positive regulation of nitrogen compound metabolic process	None	Extended
BP	GO:0051252	regulation of RNA metabolic process	None	Extended
BP	GO:0060255	regulation of macromolecule metabolic process	None	Extended
BP	GO:0060968	regulation of gene silencing	None	Extended
BP	GO:0065007	biological regulation	None	Extended
BP	GO:0070647	protein modification by small protein conjugation or removal	None	Extended
BP	GO:0071704	organic substance metabolic process	None	Extended
BP	GO:0080090	regulation of primary metabolic process	None	Extended
BP	GO:0090304	nucleic acid metabolic process	None	Extended
BP	GO:0090308	regulation of methylation-dependent chromatin silencing	None	Extended
BP	GO:0090309	positive regulation of methylation-dependent chromatin silencing	IMP	Interproscan
MF	GO:0097159	organic cyclic compound binding	None	Extended
MF	GO:0140096	catalytic activity, acting on a protein	None	Extended
MF	GO:1901265	nucleoside phosphate binding	None	Extended
BP	GO:1901360	organic cyclic compound metabolic process	None	Extended
MF	GO:1901363	heterocyclic compound binding	None	Extended
BP	GO:1901564	organonitrogen compound metabolic process	None	Extended
BP	GO:1902275	regulation of chromatin organization	None	Extended
BP	GO:1903506	regulation of nucleic acid-templated transcription	None	Extended
BP	GO:1905269	positive regulation of chromatin organization	None	Extended
BP	GO:2000112	regulation of cellular macromolecule biosynthetic process	None	Extended
BP	GO:2001141	regulation of RNA biosynthetic process	None	Extended
BP	GO:2001252	positive regulation of chromosome organization	None	Extended

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Type	GO Term	Name	Evidence	Source
MF	GO:0000217	DNA secondary structure binding	IEP	Neighborhood
CC	GO:0000228	nuclear chromosome	IEP	Neighborhood
MF	GO:0000404	heteroduplex DNA loop binding	IEP	Neighborhood
BP	GO:0000710	meiotic mismatch repair	IEP	Neighborhood
MF	GO:0001871	pattern binding	IEP	Neighborhood
MF	GO:0001872	(1->3)-beta-D-glucan binding	IEP	Neighborhood
MF	GO:0003700	DNA-binding transcription factor activity	IEP	Neighborhood
MF	GO:0003872	6-phosphofructokinase activity	IEP	Neighborhood
MF	GO:0003886	DNA (cytosine-5-)-methyltransferase activity	IEP	Neighborhood
MF	GO:0003983	UTP:glucose-1-phosphate uridylyltransferase activity	IEP	Neighborhood
MF	GO:0004609	phosphatidylserine decarboxylase activity	IEP	Neighborhood
MF	GO:0004835	tubulin-tyrosine ligase activity	IEP	Neighborhood
CC	GO:0005694	chromosome	IEP	Neighborhood
CC	GO:0005945	6-phosphofructokinase complex	IEP	Neighborhood
BP	GO:0006011	UDP-glucose metabolic process	IEP	Neighborhood
BP	GO:0006323	DNA packaging	IEP	Neighborhood
BP	GO:0006325	chromatin organization	IEP	Neighborhood
BP	GO:0006342	chromatin silencing	IEP	Neighborhood
BP	GO:0006379	mRNA cleavage	IEP	Neighborhood
BP	GO:0006479	protein methylation	IEP	Neighborhood
BP	GO:0007129	synapsis	IEP	Neighborhood
BP	GO:0008213	protein alkylation	IEP	Neighborhood
CC	GO:0008278	cohesin complex	IEP	Neighborhood
MF	GO:0008443	phosphofructokinase activity	IEP	Neighborhood
BP	GO:0008608	attachment of spindle microtubules to kinetochore	IEP	Neighborhood
MF	GO:0009008	DNA-methyltransferase activity	IEP	Neighborhood
BP	GO:0009410	response to xenobiotic stimulus	IEP	Neighborhood
BP	GO:0009566	fertilization	IEP	Neighborhood
BP	GO:0009567	double fertilization forming a zygote and endosperm	IEP	Neighborhood
BP	GO:0009890	negative regulation of biosynthetic process	IEP	Neighborhood
BP	GO:0009892	negative regulation of metabolic process	IEP	Neighborhood
BP	GO:0009954	proximal/distal pattern formation	IEP	Neighborhood
BP	GO:0010032	meiotic chromosome condensation	IEP	Neighborhood
BP	GO:0010305	leaf vascular tissue pattern formation	IEP	Neighborhood
CC	GO:0010445	nuclear dicing body	IEP	Neighborhood
MF	GO:0010491	UTP:arabinose-1-phosphate uridylyltransferase activity	IEP	Neighborhood
BP	GO:0010528	regulation of transposition	IEP	Neighborhood
BP	GO:0010529	negative regulation of transposition	IEP	Neighborhood
BP	GO:0010558	negative regulation of macromolecule biosynthetic process	IEP	Neighborhood
BP	GO:0010589	leaf proximal/distal pattern formation	IEP	Neighborhood
BP	GO:0010605	negative regulation of macromolecule metabolic process	IEP	Neighborhood
BP	GO:0010629	negative regulation of gene expression	IEP	Neighborhood
BP	GO:0016458	gene silencing	IEP	Neighborhood
BP	GO:0016569	covalent chromatin modification	IEP	Neighborhood
BP	GO:0016570	histone modification	IEP	Neighborhood
BP	GO:0016571	histone methylation	IEP	Neighborhood
MF	GO:0016755	transferase activity, transferring amino-acyl groups	IEP	Neighborhood
MF	GO:0016756	glutathione gamma-glutamylcysteinyltransferase activity	IEP	Neighborhood
MF	GO:0017103	UTP:galactose-1-phosphate uridylyltransferase activity	IEP	Neighborhood
MF	GO:0030247	polysaccharide binding	IEP	Neighborhood
BP	GO:0030261	chromosome condensation	IEP	Neighborhood
MF	GO:0030983	mismatched DNA binding	IEP	Neighborhood
BP	GO:0031047	gene silencing by RNA	IEP	Neighborhood
BP	GO:0031054	pre-miRNA processing	IEP	Neighborhood
BP	GO:0031324	negative regulation of cellular metabolic process	IEP	Neighborhood
BP	GO:0031327	negative regulation of cellular biosynthetic process	IEP	Neighborhood
MF	GO:0032135	DNA insertion or deletion binding	IEP	Neighborhood
CC	GO:0032300	mismatch repair complex	IEP	Neighborhood
BP	GO:0032879	regulation of localization	IEP	Neighborhood
BP	GO:0032880	regulation of protein localization	IEP	Neighborhood
BP	GO:0033356	UDP-L-arabinose metabolic process	IEP	Neighborhood
MF	GO:0035197	siRNA binding	IEP	Neighborhood
MF	GO:0035198	miRNA binding	IEP	Neighborhood
BP	GO:0035279	mRNA cleavage involved in gene silencing by miRNA	IEP	Neighborhood
BP	GO:0040029	regulation of gene expression, epigenetic	IEP	Neighborhood
BP	GO:0043570	maintenance of DNA repeat elements	IEP	Neighborhood
BP	GO:0043900	regulation of multi-organism process	IEP	Neighborhood
BP	GO:0045814	negative regulation of gene expression, epigenetic	IEP	Neighborhood
BP	GO:0045892	negative regulation of transcription, DNA-templated	IEP	Neighborhood
BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	IEP	Neighborhood
BP	GO:0046398	UDP-glucuronate metabolic process	IEP	Neighborhood
BP	GO:0046937	phytochelatin metabolic process	IEP	Neighborhood
BP	GO:0046938	phytochelatin biosynthetic process	IEP	Neighborhood
MF	GO:0047268	galactinol-raffinose galactosyltransferase activity	IEP	Neighborhood
MF	GO:0047338	UTP:xylose-1-phosphate uridylyltransferase activity	IEP	Neighborhood
MF	GO:0047350	glucuronate-1-phosphate uridylyltransferase activity	IEP	Neighborhood
BP	GO:0048240	sperm capacitation	IEP	Neighborhood
BP	GO:0048444	floral organ morphogenesis	IEP	Neighborhood
BP	GO:0048449	floral organ formation	IEP	Neighborhood
BP	GO:0048451	petal formation	IEP	Neighborhood
BP	GO:0048453	sepal formation	IEP	Neighborhood
BP	GO:0048481	plant ovule development	IEP	Neighborhood
BP	GO:0048646	anatomical structure formation involved in morphogenesis	IEP	Neighborhood
BP	GO:0051172	negative regulation of nitrogen compound metabolic process	IEP	Neighborhood
BP	GO:0051177	meiotic sister chromatid cohesion	IEP	Neighborhood
BP	GO:0051253	negative regulation of RNA metabolic process	IEP	Neighborhood
BP	GO:0051316	attachment of spindle microtubules to kinetochore involved in meiotic chromosome segregation	IEP	Neighborhood
BP	GO:0051455	attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation	IEP	Neighborhood
MF	GO:0051748	UTP-monosaccharide-1-phosphate uridylyltransferase activity	IEP	Neighborhood
BP	GO:0051754	meiotic sister chromatid cohesion, centromeric	IEP	Neighborhood
BP	GO:0052573	UDP-D-galactose metabolic process	IEP	Neighborhood
BP	GO:0060341	regulation of cellular localization	IEP	Neighborhood
MF	GO:0061980	regulatory RNA binding	IEP	Neighborhood
BP	GO:0070192	chromosome organization involved in meiotic cell cycle	IEP	Neighborhood
MF	GO:0070569	uridylyltransferase activity	IEP	Neighborhood
BP	GO:0070601	centromeric sister chromatid cohesion	IEP	Neighborhood
BP	GO:0080154	regulation of fertilization	IEP	Neighborhood
BP	GO:0080155	regulation of double fertilization forming a zygote and endosperm	IEP	Neighborhood
BP	GO:0080188	RNA-directed DNA methylation	IEP	Neighborhood
BP	GO:0090305	nucleic acid phosphodiester bond hydrolysis	IEP	Neighborhood
BP	GO:0090501	RNA phosphodiester bond hydrolysis	IEP	Neighborhood
BP	GO:0090697	post-embryonic plant organ morphogenesis	IEP	Neighborhood
BP	GO:0098795	mRNA cleavage involved in gene silencing	IEP	Neighborhood
MF	GO:0140110	transcription regulator activity	IEP	Neighborhood
BP	GO:1902679	negative regulation of RNA biosynthetic process	IEP	Neighborhood
BP	GO:1903507	negative regulation of nucleic acid-templated transcription	IEP	Neighborhood
BP	GO:1903827	regulation of cellular protein localization	IEP	Neighborhood
BP	GO:1905393	plant organ formation	IEP	Neighborhood
CC	GO:1990391	DNA repair complex	IEP	Neighborhood
BP	GO:2000008	regulation of protein localization to cell surface	IEP	Neighborhood
BP	GO:2000113	negative regulation of cellular macromolecule biosynthetic process	IEP	Neighborhood
BP	GO:2000241	regulation of reproductive process	IEP	Neighborhood

InterPro domains	Description	Start	Stop
IPR003105	SRA_YDG	260	410
IPR027370	Znf-RING_LisH	495	537

External Links

No external refs found!

AT5G39550 (VIM3, ORTH1)

Expression Profile

Co-expression Networks

Expression Context Conservation (ECC)

Functional Annotation