AT2G39140

Description : pseudouridine synthase family protein

Gene families : OG_01_0004197 (OrthoFinder output from Ath, Cre, Mpo, Ppa and Zci) Phylogenetic Tree(s): OG0004197_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: AT2G39140
Cluster	HCCA: Cluster_135

Target	Alias	Description	ECC score	Gene Family Method	Actions
Cre02.g095121	No alias	RNA processing.RNA...	0.03	OrthoFinder output from Ath, Cre, Mpo, Ppa and Zci
Pp3c7_13640V3.1	No alias	pseudouridine synthase family protein	0.13	OrthoFinder output from Ath, Cre, Mpo, Ppa and Zci

Type	GO Term	Name	Evidence	Source
BP	GO:0000470	maturation of LSU-rRNA	None	Extended
BP	GO:0000488	maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA)	IMP	Interproscan
BP	GO:0000489	maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA)	IMP	Interproscan
MF	GO:0003674	molecular_function	None	Extended
MF	GO:0003676	nucleic acid binding	None	Extended
MF	GO:0003723	RNA binding	ISS	Interproscan
MF	GO:0003824	catalytic activity	None	Extended
MF	GO:0005488	binding	None	Extended
CC	GO:0005575	cellular_component	None	Extended
BP	GO:0006139	nucleobase-containing compound metabolic process	None	Extended
BP	GO:0006364	rRNA processing	None	Extended
BP	GO:0006396	RNA processing	None	Extended
BP	GO:0006412	translation	None	Extended
BP	GO:0006518	peptide metabolic process	None	Extended
BP	GO:0006725	cellular aromatic compound metabolic process	None	Extended
BP	GO:0006807	nitrogen compound metabolic process	None	Extended
BP	GO:0006996	organelle organization	None	Extended
BP	GO:0008150	biological_process	None	Extended
BP	GO:0008152	metabolic process	None	Extended
BP	GO:0009058	biosynthetic process	None	Extended
BP	GO:0009059	macromolecule biosynthetic process	None	Extended
CC	GO:0009501	amyloplast	TAS	Interproscan
CC	GO:0009507	chloroplast	IDA	Interproscan
CC	GO:0009507	chloroplast	ISM	Interproscan
CC	GO:0009536	plastid	None	Extended
BP	GO:0009657	plastid organization	None	Extended
MF	GO:0009982	pseudouridine synthase activity	TAS	Interproscan
BP	GO:0009987	cellular process	None	Extended
BP	GO:0016043	cellular component organization	None	Extended
BP	GO:0016070	RNA metabolic process	None	Extended
BP	GO:0016072	rRNA metabolic process	None	Extended
MF	GO:0016853	isomerase activity	None	Extended
MF	GO:0016866	intramolecular transferase activity	None	Extended
BP	GO:0019538	protein metabolic process	None	Extended
BP	GO:0030490	maturation of SSU-rRNA	None	Extended
BP	GO:0032544	plastid translation	IMP	Interproscan
BP	GO:0034470	ncRNA processing	None	Extended
BP	GO:0034641	cellular nitrogen compound metabolic process	None	Extended
BP	GO:0034645	cellular macromolecule biosynthetic process	None	Extended
BP	GO:0034660	ncRNA metabolic process	None	Extended
BP	GO:0043043	peptide biosynthetic process	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:0043603	cellular amide metabolic process	None	Extended
BP	GO:0043604	amide biosynthetic process	None	Extended
BP	GO:0044237	cellular metabolic process	None	Extended
BP	GO:0044238	primary metabolic process	None	Extended
BP	GO:0044249	cellular biosynthetic process	None	Extended
BP	GO:0044260	cellular macromolecule metabolic process	None	Extended
BP	GO:0044267	cellular protein metabolic process	None	Extended
BP	GO:0044271	cellular nitrogen compound biosynthetic process	None	Extended
BP	GO:0046483	heterocycle metabolic process	None	Extended
BP	GO:0071704	organic substance metabolic process	None	Extended
BP	GO:0071840	cellular component organization or biogenesis	None	Extended
BP	GO:0090304	nucleic acid metabolic process	None	Extended
MF	GO:0097159	organic cyclic compound binding	None	Extended
CC	GO:0110165	cellular anatomical entity	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:1901566	organonitrogen compound biosynthetic process	None	Extended
BP	GO:1901576	organic substance biosynthetic process	None	Extended

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Type	GO Term	Name	Evidence	Source
MF	GO:0000095	S-adenosyl-L-methionine transmembrane transporter activity	IEP	HCCA
MF	GO:0000166	nucleotide binding	IEP	HCCA
BP	GO:0000304	response to singlet oxygen	IEP	HCCA
BP	GO:0003006	developmental process involved in reproduction	IEP	HCCA
MF	GO:0003724	RNA helicase activity	IEP	HCCA
MF	GO:0004045	aminoacyl-tRNA hydrolase activity	IEP	HCCA
MF	GO:0004326	tetrahydrofolylpolyglutamate synthase activity	IEP	HCCA
MF	GO:0005524	ATP binding	IEP	HCCA
CC	GO:0005694	chromosome	IEP	HCCA
CC	GO:0005739	mitochondrion	IEP	HCCA
CC	GO:0005743	mitochondrial inner membrane	IEP	HCCA
CC	GO:0005759	mitochondrial matrix	IEP	HCCA
BP	GO:0006081	cellular aldehyde metabolic process	IEP	HCCA
BP	GO:0006082	organic acid metabolic process	IEP	HCCA
BP	GO:0006090	pyruvate metabolic process	IEP	HCCA
BP	GO:0006351	transcription, DNA-templated	IEP	HCCA
BP	GO:0006355	regulation of transcription, DNA-templated	IEP	HCCA
BP	GO:0006399	tRNA metabolic process	IEP	HCCA
BP	GO:0006520	cellular amino acid metabolic process	IEP	HCCA
BP	GO:0006605	protein targeting	IEP	HCCA
BP	GO:0006644	phospholipid metabolic process	IEP	HCCA
BP	GO:0006650	glycerophospholipid metabolic process	IEP	HCCA
BP	GO:0006655	phosphatidylglycerol biosynthetic process	IEP	HCCA
BP	GO:0006730	one-carbon metabolic process	IEP	HCCA
BP	GO:0006778	porphyrin-containing compound metabolic process	IEP	HCCA
BP	GO:0006779	porphyrin-containing compound biosynthetic process	IEP	HCCA
BP	GO:0006783	heme biosynthetic process	IEP	HCCA
BP	GO:0006790	sulfur compound metabolic process	IEP	HCCA
BP	GO:0006793	phosphorus metabolic process	IEP	HCCA
BP	GO:0006796	phosphate-containing compound metabolic process	IEP	HCCA
BP	GO:0006810	transport	IEP	HCCA
BP	GO:0006839	mitochondrial transport	IEP	HCCA
BP	GO:0006886	intracellular protein transport	IEP	HCCA
BP	GO:0007275	multicellular organism development	IEP	HCCA
BP	GO:0008033	tRNA processing	IEP	HCCA
BP	GO:0008104	protein localization	IEP	HCCA
MF	GO:0008186	ATP-dependent activity, acting on RNA	IEP	HCCA
MF	GO:0008187	poly-pyrimidine tract binding	IEP	HCCA
MF	GO:0008235	metalloexopeptidase activity	IEP	HCCA
MF	GO:0008237	metallopeptidase activity	IEP	HCCA
MF	GO:0008266	poly(U) RNA binding	IEP	HCCA
BP	GO:0008610	lipid biosynthetic process	IEP	HCCA
BP	GO:0008654	phospholipid biosynthetic process	IEP	HCCA
MF	GO:0009041	uridylate kinase activity	IEP	HCCA
BP	GO:0009072	aromatic amino acid family metabolic process	IEP	HCCA
BP	GO:0009073	aromatic amino acid family biosynthetic process	IEP	HCCA
BP	GO:0009240	isopentenyl diphosphate biosynthetic process	IEP	HCCA
CC	GO:0009295	nucleoid	IEP	HCCA
BP	GO:0009451	RNA modification	IEP	HCCA
CC	GO:0009508	plastid chromosome	IEP	HCCA
CC	GO:0009526	plastid envelope	IEP	HCCA
CC	GO:0009528	plastid inner membrane	IEP	HCCA
CC	GO:0009532	plastid stroma	IEP	HCCA
CC	GO:0009534	chloroplast thylakoid	IEP	HCCA
CC	GO:0009570	chloroplast stroma	IEP	HCCA
BP	GO:0009631	cold acclimation	IEP	HCCA
BP	GO:0009653	anatomical structure morphogenesis	IEP	HCCA
BP	GO:0009658	chloroplast organization	IEP	HCCA
BP	GO:0009663	plasmodesma organization	IEP	HCCA
BP	GO:0009668	plastid membrane organization	IEP	HCCA
CC	GO:0009706	chloroplast inner membrane	IEP	HCCA
BP	GO:0009790	embryo development	IEP	HCCA
BP	GO:0009793	embryo development ending in seed dormancy	IEP	HCCA
BP	GO:0009889	regulation of biosynthetic process	IEP	HCCA
BP	GO:0009891	positive regulation of biosynthetic process	IEP	HCCA
BP	GO:0009893	positive regulation of metabolic process	IEP	HCCA
BP	GO:0009894	regulation of catabolic process	IEP	HCCA
BP	GO:0009895	negative regulation of catabolic process	IEP	HCCA
BP	GO:0009902	chloroplast relocation	IEP	HCCA
CC	GO:0009941	chloroplast envelope	IEP	HCCA
BP	GO:0009965	leaf morphogenesis	IEP	HCCA
BP	GO:0010020	chloroplast fission	IEP	HCCA
BP	GO:0010027	thylakoid membrane organization	IEP	HCCA
BP	GO:0010103	stomatal complex morphogenesis	IEP	HCCA
BP	GO:0010207	photosystem II assembly	IEP	HCCA
BP	GO:0010468	regulation of gene expression	IEP	HCCA
BP	GO:0010496	intercellular transport	IEP	HCCA
BP	GO:0010497	plasmodesmata-mediated intercellular transport	IEP	HCCA
BP	GO:0010556	regulation of macromolecule biosynthetic process	IEP	HCCA
BP	GO:0010557	positive regulation of macromolecule biosynthetic process	IEP	HCCA
BP	GO:0010604	positive regulation of macromolecule metabolic process	IEP	HCCA
BP	GO:0010608	posttranscriptional regulation of gene expression	IEP	HCCA
BP	GO:0015031	protein transport	IEP	HCCA
MF	GO:0015101	organic cation transmembrane transporter activity	IEP	HCCA
BP	GO:0015695	organic cation transport	IEP	HCCA
BP	GO:0015805	S-adenosyl-L-methionine transport	IEP	HCCA
BP	GO:0016053	organic acid biosynthetic process	IEP	HCCA
BP	GO:0016071	mRNA metabolic process	IEP	HCCA
BP	GO:0016226	iron-sulfur cluster assembly	IEP	HCCA
BP	GO:0016556	mRNA modification	IEP	HCCA
MF	GO:0016776	phosphotransferase activity, phosphate group as acceptor	IEP	HCCA
MF	GO:0016874	ligase activity	IEP	HCCA
MF	GO:0016881	acid-amino acid ligase activity	IEP	HCCA
MF	GO:0017076	purine nucleotide binding	IEP	HCCA
BP	GO:0018130	heterocycle biosynthetic process	IEP	HCCA
MF	GO:0019205	nucleobase-containing compound kinase activity	IEP	HCCA
BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	IEP	HCCA
BP	GO:0019220	regulation of phosphate metabolic process	IEP	HCCA
BP	GO:0019222	regulation of metabolic process	IEP	HCCA
BP	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	IEP	HCCA
BP	GO:0019438	aromatic compound biosynthetic process	IEP	HCCA
BP	GO:0019637	organophosphate metabolic process	IEP	HCCA
BP	GO:0019682	glyceraldehyde-3-phosphate metabolic process	IEP	HCCA
BP	GO:0019750	chloroplast localization	IEP	HCCA
BP	GO:0019752	carboxylic acid metabolic process	IEP	HCCA
CC	GO:0019866	organelle inner membrane	IEP	HCCA
BP	GO:0022414	reproductive process	IEP	HCCA
BP	GO:0022607	cellular component assembly	IEP	HCCA
BP	GO:0030154	cell differentiation	IEP	HCCA
MF	GO:0030554	adenyl nucleotide binding	IEP	HCCA
CC	GO:0031090	organelle membrane	IEP	HCCA
BP	GO:0031163	metallo-sulfur cluster assembly	IEP	HCCA
BP	GO:0031323	regulation of cellular metabolic process	IEP	HCCA
BP	GO:0031325	positive regulation of cellular metabolic process	IEP	HCCA
BP	GO:0031326	regulation of cellular biosynthetic process	IEP	HCCA
BP	GO:0031328	positive regulation of cellular biosynthetic process	IEP	HCCA
BP	GO:0031329	regulation of cellular catabolic process	IEP	HCCA
BP	GO:0031330	negative regulation of cellular catabolic process	IEP	HCCA
BP	GO:0031399	regulation of protein modification process	IEP	HCCA
BP	GO:0031407	oxylipin metabolic process	IEP	HCCA
BP	GO:0031408	oxylipin biosynthetic process	IEP	HCCA
CC	GO:0031966	mitochondrial membrane	IEP	HCCA
CC	GO:0031967	organelle envelope	IEP	HCCA
CC	GO:0031969	chloroplast membrane	IEP	HCCA
CC	GO:0031975	envelope	IEP	HCCA
CC	GO:0031976	plastid thylakoid	IEP	HCCA
BP	GO:0032501	multicellular organismal process	IEP	HCCA
BP	GO:0032502	developmental process	IEP	HCCA
MF	GO:0032553	ribonucleotide binding	IEP	HCCA
MF	GO:0032555	purine ribonucleotide binding	IEP	HCCA
MF	GO:0032559	adenyl ribonucleotide binding	IEP	HCCA
BP	GO:0032774	RNA biosynthetic process	IEP	HCCA
BP	GO:0032787	monocarboxylic acid metabolic process	IEP	HCCA
BP	GO:0033013	tetrapyrrole metabolic process	IEP	HCCA
BP	GO:0033014	tetrapyrrole biosynthetic process	IEP	HCCA
BP	GO:0033036	macromolecule localization	IEP	HCCA
BP	GO:0033365	protein localization to organelle	IEP	HCCA
BP	GO:0034330	cell junction organization	IEP	HCCA
BP	GO:0034613	cellular protein localization	IEP	HCCA
BP	GO:0034622	cellular protein-containing complex assembly	IEP	HCCA
BP	GO:0034654	nucleobase-containing compound biosynthetic process	IEP	HCCA
BP	GO:0035303	regulation of dephosphorylation	IEP	HCCA
BP	GO:0035304	regulation of protein dephosphorylation	IEP	HCCA
MF	GO:0035639	purine ribonucleoside triphosphate binding	IEP	HCCA
BP	GO:0042168	heme metabolic process	IEP	HCCA
CC	GO:0042170	plastid membrane	IEP	HCCA
BP	GO:0042793	plastid transcription	IEP	HCCA
MF	GO:0043168	anion binding	IEP	HCCA
BP	GO:0043412	macromolecule modification	IEP	HCCA
BP	GO:0043436	oxoacid metabolic process	IEP	HCCA
BP	GO:0043487	regulation of RNA stability	IEP	HCCA
BP	GO:0043489	RNA stabilization	IEP	HCCA
BP	GO:0043572	plastid fission	IEP	HCCA
BP	GO:0043933	protein-containing complex subunit organization	IEP	HCCA
BP	GO:0044255	cellular lipid metabolic process	IEP	HCCA
BP	GO:0044281	small molecule metabolic process	IEP	HCCA
BP	GO:0044283	small molecule biosynthetic process	IEP	HCCA
BP	GO:0045017	glycerolipid biosynthetic process	IEP	HCCA
BP	GO:0045036	protein targeting to chloroplast	IEP	HCCA
BP	GO:0045037	protein import into chloroplast stroma	IEP	HCCA
BP	GO:0045184	establishment of protein localization	IEP	HCCA
BP	GO:0045216	cell-cell junction organization	IEP	HCCA
BP	GO:0045893	positive regulation of transcription, DNA-templated	IEP	HCCA
BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	IEP	HCCA
BP	GO:0046148	pigment biosynthetic process	IEP	HCCA
BP	GO:0046471	phosphatidylglycerol metabolic process	IEP	HCCA
BP	GO:0046474	glycerophospholipid biosynthetic process	IEP	HCCA
BP	GO:0046486	glycerolipid metabolic process	IEP	HCCA
BP	GO:0046490	isopentenyl diphosphate metabolic process	IEP	HCCA
BP	GO:0046907	intracellular transport	IEP	HCCA
BP	GO:0048481	plant ovule development	IEP	HCCA
BP	GO:0048518	positive regulation of biological process	IEP	HCCA
BP	GO:0048522	positive regulation of cellular process	IEP	HCCA
BP	GO:0048856	anatomical structure development	IEP	HCCA
MF	GO:0050145	nucleoside monophosphate kinase activity	IEP	HCCA
BP	GO:0051171	regulation of nitrogen compound metabolic process	IEP	HCCA
BP	GO:0051173	positive regulation of nitrogen compound metabolic process	IEP	HCCA
BP	GO:0051174	regulation of phosphorus metabolic process	IEP	HCCA
BP	GO:0051179	localization	IEP	HCCA
BP	GO:0051234	establishment of localization	IEP	HCCA
BP	GO:0051252	regulation of RNA metabolic process	IEP	HCCA
BP	GO:0051254	positive regulation of RNA metabolic process	IEP	HCCA
BP	GO:0051640	organelle localization	IEP	HCCA
BP	GO:0051641	cellular localization	IEP	HCCA
BP	GO:0051644	plastid localization	IEP	HCCA
BP	GO:0051649	establishment of localization in cell	IEP	HCCA
BP	GO:0051656	establishment of organelle localization	IEP	HCCA
BP	GO:0051667	establishment of plastid localization	IEP	HCCA
MF	GO:0052381	tRNA dimethylallyltransferase activity	IEP	HCCA
BP	GO:0060255	regulation of macromolecule metabolic process	IEP	HCCA
BP	GO:0061024	membrane organization	IEP	HCCA
BP	GO:0065003	protein-containing complex assembly	IEP	HCCA
BP	GO:0070727	cellular macromolecule localization	IEP	HCCA
BP	GO:0071702	organic substance transport	IEP	HCCA
BP	GO:0071705	nitrogen compound transport	IEP	HCCA
BP	GO:0072348	sulfur compound transport	IEP	HCCA
BP	GO:0072594	establishment of protein localization to organelle	IEP	HCCA
BP	GO:0072596	establishment of protein localization to chloroplast	IEP	HCCA
BP	GO:0072598	protein localization to chloroplast	IEP	HCCA
BP	GO:0080090	regulation of primary metabolic process	IEP	HCCA
BP	GO:0090351	seedling development	IEP	HCCA
BP	GO:0090407	organophosphate biosynthetic process	IEP	HCCA
BP	GO:0090626	plant epidermis morphogenesis	IEP	HCCA
MF	GO:0097367	carbohydrate derivative binding	IEP	HCCA
BP	GO:0097659	nucleic acid-templated transcription	IEP	HCCA
MF	GO:0140098	catalytic activity, acting on RNA	IEP	HCCA
MF	GO:0140101	catalytic activity, acting on a tRNA	IEP	HCCA
MF	GO:0140640	catalytic activity, acting on a nucleic acid	IEP	HCCA
BP	GO:1900865	chloroplast RNA modification	IEP	HCCA
MF	GO:1901265	nucleoside phosphate binding	IEP	HCCA
BP	GO:1901362	organic cyclic compound biosynthetic process	IEP	HCCA
MF	GO:1901682	sulfur compound transmembrane transporter activity	IEP	HCCA
BP	GO:1902369	negative regulation of RNA catabolic process	IEP	HCCA
BP	GO:1902680	positive regulation of RNA biosynthetic process	IEP	HCCA
BP	GO:1903506	regulation of nucleic acid-templated transcription	IEP	HCCA
BP	GO:1903508	positive regulation of nucleic acid-templated transcription	IEP	HCCA
BP	GO:1905392	plant organ morphogenesis	IEP	HCCA
BP	GO:2000112	regulation of cellular macromolecule biosynthetic process	IEP	HCCA
BP	GO:2001141	regulation of RNA biosynthetic process	IEP	HCCA

InterPro domains	Description	Start	Stop
IPR006145	PsdUridine_synth_RsuA/RluA	223	364
IPR002942	S4_RNA-bd	160	203

External Links

PLAZA 3.0 Dicots	AT2G39140

AT2G39140

Expression Profile

Co-expression Networks

Expression Context Conservation (ECC)

Functional Annotation