evm.model.tig00020961.8

Description : (at4g09730 : 256.0) Encodes RH39, a DEAD-box protein involved in the introduction of the hidden break into the 23S rRNA in the chloroplasts. Recombinant RH39 binds to the 23S rRNA in a segment adjacent to the stem-loop creating the hidden break target loop in a sequence-dependent manner. Has ATP-hydrolyzing activity at a Kcat of 5.3 /min in the presence of rRNA sequence. Mutants have drastically reduced level of level of ribulose 1,5-bisphosphate carboxylase/oxygenase.; RH39 (RH39); FUNCTIONS IN: LSU rRNA binding, ATPase activity, ATP-dependent helicase activity; INVOLVED IN: chloroplast ribulose bisphosphate carboxylase complex biogenesis, chloroplast rRNA processing; LOCATED IN: chloroplast; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA helicase, DEAD-box type, Q motif (InterPro:IPR014014), DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: DEA(D/H)-box RNA helicase family protein (TAIR:AT3G06980.1); Has 40425 Blast hits to 39698 proteins in 3032 species: Archae - 675; Bacteria - 19989; Metazoa - 5933; Fungi - 4498; Plants - 2407; Viruses - 9; Other Eukaryotes - 6914 (source: NCBI BLink). & (p46942|db10_nicsy : 124.0) ATP-dependent RNA helicase-like protein DB10 (EC 3.6.1.-) - Nicotiana sylvestris (Wood tobacco) & (reliability: 512.0) & (original description: no original description)

Gene families : OG_42_0007585 (Orthogroups_2024-Update) Phylogenetic Tree(s): OG0007585_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	Cyanophora release: evm.model.tig00020961.8
Cluster	HCCA clusters: Cluster_32

Target	Alias	Description	ECC score	Gene Family Method
86079	No alias	RH39	0.02	Orthogroups_2024-Update
A4A49_11215	No alias	dead-box atp-dependent rna helicase 39	0.01	Orthogroups_2024-Update
Bradi2g05390	No alias	RH39	0.02	Orthogroups_2024-Update
Cre01.g033832	No alias	RH39	0.03	Orthogroups_2024-Update
Glyma.02G078100	No alias	RH39	0.02	Orthogroups_2024-Update
Mp5g09580.1	No alias	DEAD-box ATP-dependent RNA helicase 39 OS=Oryza sativa...	0.01	Orthogroups_2024-Update
Seita.5G131500.1	No alias	23S-rRNA maturation helicase *(RH39)	0.02	Orthogroups_2024-Update
Sobic.003G039300.1	No alias	23S-rRNA maturation helicase *(RH39)	0.03	Orthogroups_2024-Update

Type	GO Term	Name	Evidence	Source
MF	GO:0000166	nucleotide binding	None	Extended
MF	GO:0003674	molecular_function	None	Extended
MF	GO:0003676	nucleic acid binding	IEA	InterProScan predictions
MF	GO:0003723	RNA binding	None	Extended
MF	GO:0003747	translation release factor activity	IEA	InterProScan predictions
MF	GO:0005488	binding	None	Extended
MF	GO:0005524	ATP binding	IEA	InterProScan predictions
BP	GO:0006415	translational termination	IEA	InterProScan predictions
MF	GO:0008079	translation termination factor activity	None	Extended
MF	GO:0008135	translation factor activity, RNA binding	None	Extended
MF	GO:0008144	drug binding	None	Extended
BP	GO:0008150	biological_process	None	Extended
BP	GO:0009987	cellular process	None	Extended
BP	GO:0016043	cellular component organization	None	Extended
MF	GO:0017076	purine nucleotide binding	None	Extended
BP	GO:0022411	cellular component disassembly	None	Extended
MF	GO:0030554	adenyl nucleotide binding	None	Extended
MF	GO:0032553	ribonucleotide binding	None	Extended
MF	GO:0032555	purine ribonucleotide binding	None	Extended
MF	GO:0032559	adenyl ribonucleotide binding	None	Extended
BP	GO:0032984	protein-containing complex disassembly	None	Extended
MF	GO:0035639	purine ribonucleoside triphosphate binding	None	Extended
MF	GO:0036094	small molecule binding	None	Extended
MF	GO:0043167	ion binding	None	Extended
MF	GO:0043168	anion binding	None	Extended
BP	GO:0043624	cellular protein complex disassembly	None	Extended
BP	GO:0043933	protein-containing complex subunit organization	None	Extended
BP	GO:0071840	cellular component organization or biogenesis	None	Extended
MF	GO:0097159	organic cyclic compound binding	None	Extended
MF	GO:0097367	carbohydrate derivative binding	None	Extended
MF	GO:1901265	nucleoside phosphate binding	None	Extended
MF	GO:1901363	heterocyclic compound binding	None	Extended

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Type	GO Term	Name	Evidence	Source
MF	GO:0000062	fatty-acyl-CoA binding	IEP	Predicted GO
MF	GO:0003746	translation elongation factor activity	IEP	Predicted GO
MF	GO:0003824	catalytic activity	IEP	Predicted GO
MF	GO:0004066	asparagine synthase (glutamine-hydrolyzing) activity	IEP	Predicted GO
MF	GO:0004356	glutamate-ammonia ligase activity	IEP	Predicted GO
MF	GO:0004359	glutaminase activity	IEP	Predicted GO
MF	GO:0004478	methionine adenosyltransferase activity	IEP	Predicted GO
MF	GO:0004590	orotidine-5'-phosphate decarboxylase activity	IEP	Predicted GO
BP	GO:0006206	pyrimidine nucleobase metabolic process	IEP	Predicted GO
BP	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	IEP	Predicted GO
BP	GO:0006334	nucleosome assembly	IEP	Predicted GO
BP	GO:0006414	translational elongation	IEP	Predicted GO
BP	GO:0006520	cellular amino acid metabolic process	IEP	Predicted GO
BP	GO:0006528	asparagine metabolic process	IEP	Predicted GO
BP	GO:0006529	asparagine biosynthetic process	IEP	Predicted GO
BP	GO:0006541	glutamine metabolic process	IEP	Predicted GO
BP	GO:0006556	S-adenosylmethionine biosynthetic process	IEP	Predicted GO
BP	GO:0006807	nitrogen compound metabolic process	IEP	Predicted GO
BP	GO:0008152	metabolic process	IEP	Predicted GO
MF	GO:0008168	methyltransferase activity	IEP	Predicted GO
MF	GO:0008173	RNA methyltransferase activity	IEP	Predicted GO
MF	GO:0008483	transaminase activity	IEP	Predicted GO
BP	GO:0009064	glutamine family amino acid metabolic process	IEP	Predicted GO
BP	GO:0009066	aspartate family amino acid metabolic process	IEP	Predicted GO
BP	GO:0009067	aspartate family amino acid biosynthetic process	IEP	Predicted GO
BP	GO:0009112	nucleobase metabolic process	IEP	Predicted GO
BP	GO:0009116	nucleoside metabolic process	IEP	Predicted GO
MF	GO:0010309	acireductone dioxygenase [iron(II)-requiring] activity	IEP	Predicted GO
MF	GO:0016211	ammonia ligase activity	IEP	Predicted GO
MF	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	IEP	Predicted GO
MF	GO:0016740	transferase activity	IEP	Predicted GO
MF	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	IEP	Predicted GO
MF	GO:0016769	transferase activity, transferring nitrogenous groups	IEP	Predicted GO
MF	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	IEP	Predicted GO
MF	GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	IEP	Predicted GO
MF	GO:0016831	carboxy-lyase activity	IEP	Predicted GO
MF	GO:0016879	ligase activity, forming carbon-nitrogen bonds	IEP	Predicted GO
MF	GO:0016880	acid-ammonia (or amide) ligase activity	IEP	Predicted GO
MF	GO:0016884	carbon-nitrogen ligase activity, with glutamine as amido-N-donor	IEP	Predicted GO
BP	GO:0019856	pyrimidine nucleobase biosynthetic process	IEP	Predicted GO
BP	GO:0030258	lipid modification	IEP	Predicted GO
CC	GO:0030684	preribosome	IEP	Predicted GO
CC	GO:0030688	preribosome, small subunit precursor	IEP	Predicted GO
MF	GO:0033218	amide binding	IEP	Predicted GO
BP	GO:0034728	nucleosome organization	IEP	Predicted GO
BP	GO:0044237	cellular metabolic process	IEP	Predicted GO
BP	GO:0044281	small molecule metabolic process	IEP	Predicted GO
BP	GO:0046112	nucleobase biosynthetic process	IEP	Predicted GO
BP	GO:0046500	S-adenosylmethionine metabolic process	IEP	Predicted GO
BP	GO:0046834	lipid phosphorylation	IEP	Predicted GO
BP	GO:0046854	phosphatidylinositol phosphorylation	IEP	Predicted GO
MF	GO:0048037	cofactor binding	IEP	Predicted GO
MF	GO:0051213	dioxygenase activity	IEP	Predicted GO
BP	GO:0065004	protein-DNA complex assembly	IEP	Predicted GO
BP	GO:0071704	organic substance metabolic process	IEP	Predicted GO
BP	GO:0071824	protein-DNA complex subunit organization	IEP	Predicted GO
BP	GO:0072527	pyrimidine-containing compound metabolic process	IEP	Predicted GO
BP	GO:0072528	pyrimidine-containing compound biosynthetic process	IEP	Predicted GO
BP	GO:1901135	carbohydrate derivative metabolic process	IEP	Predicted GO
MF	GO:1901567	fatty acid derivative binding	IEP	Predicted GO
BP	GO:1901605	alpha-amino acid metabolic process	IEP	Predicted GO
BP	GO:1901657	glycosyl compound metabolic process	IEP	Predicted GO

InterPro domains	Description	Start	Stop
IPR001650	Helicase_C	293	385
IPR011545	DEAD/DEAH_box_helicase_dom	97	199
IPR000352	Pep_chain_release_fac_I_II	816	907
IPR005139	PCRF	638	708

External Links

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evm.model.tig00020961.8

Expression Profile

Co-expression Networks

Expression Context Conservation (ECC)

Functional Annotation