RNASEK ribonuclease K [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNASEKprovided by HGNC
Official Full Name: ribonuclease Kprovided by HGNC
Primary source: HGNC:HGNC:33911
See related: Ensembl:ENSG00000219200 MIM:617098; AllianceGenome:HGNC:33911
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Enables RNA endonuclease activity. Involved in endosomal lumen acidification; proton transmembrane transport; and receptor-mediated endocytosis of virus by host cell. Part of membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in adrenal (RPKM 84.0), kidney (RPKM 67.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (7012624..7014532)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (6913249..6915130)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (6915943..6917851)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of novel alternative transcripts of the human Ribonuclease kappa (RNASEK) gene using 3' RACE and high-throughput sequencing approaches.
Title: Identification of novel alternative transcripts of the human Ribonuclease κ (RNASEK) gene using 3' RACE and high-throughput sequencing approaches.
Low Rnase K expression is associated with prostate cancer.
Title: Expressional profiling and clinical relevance of RNase κ in prostate cancer: a novel indicator of favorable progression-free survival.
Analyses of global gene expression data from adipose tissue, skeletal muscle, and whole blood provide evidence that rs75493593 is associated with RNASEK gene expression, suggesting that RNASEK expression may mediate the effect of genotype on diabetes.
Title: Analysis of SLC16A11 Variants in 12,811 American Indians: Genotype-Obesity Interaction for Type 2 Diabetes and an Association With RNASEK Expression.
RNASEK closely associates with the V-ATPase and is required for its function; its loss prevents the early events of endocytosis and the replication of multiple pathogenic viruses.
Title: RNASEK Is a V-ATPase-Associated Factor Required for Endocytosis and the Replication of Rhinovirus, Influenza A Virus, and Dengue Virus.
Data suggest that the Cys6-Cys69 disulfide bond is likely to exist in all RNase kappa family members, including human.
Title: Essential cysteine residues for human RNase κ catalytic activity.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Based on sequence alignment and substrate specificity data, as well as the resistance of the protein to the placental ribonuclease inhibitor, the human RNase kappa may be a novel endoribonuclease distinct from other known ribonucleases.
Title: Molecular cloning and characterization of the human RNase kappa, an ortholog of Cc RNase.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC156606P3 (e-PCR)
- UniSTS:271410

PMC156606P4 (e-PCR)
- UniSTS:271411

MARC_24292-24293:1030106971:1 (e-PCR)
- UniSTS:268876

SGC33235 (e-PCR)
- UniSTS:40557

D15S1477 (e-PCR)
- UniSTS:474482

Readthrough RNASEK-C17orf49

Readthrough gene: RNASEK-C17orf49, Included gene: BACC1

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA endonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi lumen acidification	NAS Non-traceable Author Statement more info	PubMed
involved_in endosomal lumen acidification	IPI Inferred from Physical Interaction more info	PubMed
involved_in endosomal lumen acidification	NAS Non-traceable Author Statement more info	PubMed
involved_in intracellular pH reduction	NAS Non-traceable Author Statement more info	PubMed
involved_in lysosomal lumen acidification	NAS Non-traceable Author Statement more info	PubMed
involved_in proton transmembrane transport	IPI Inferred from Physical Interaction more info	PubMed
involved_in proton transmembrane transport	NAS Non-traceable Author Statement more info	PubMed
involved_in receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor-mediated endocytosis of virus by host cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vacuolar acidification	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi membrane	NAS Non-traceable Author Statement more info	PubMed
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	NAS Non-traceable Author Statement more info	PubMed
located_in lysosomal membrane	NAS Non-traceable Author Statement more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
part_of proton-transporting V-type ATPase complex	NAS Non-traceable Author Statement more info	PubMed
part_of vacuolar proton-transporting V-type ATPase, V0 domain	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ribonuclease kappa

Names: RNase kappa; V-ATPase subunit f; V-type proton ATPase subunit f; ribonuclease, RNase K

NP_001004333.3

EC 3.1.-.-

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001004333.5 → NP_001004333.3 ribonuclease kappa

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the supported protein.

Source sequence(s)

AC040977

Consensus CDS

CCDS45594.3

UniProtKB/TrEMBL

A0A0C4DH89

Related

ENSP00000468923.2, ENST00000593646.6

RNA

NR_037715.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) includes an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AA633512, BC070349, BM835723, BQ223829, CD176288

Related

ENST00000549393.2
NR_037716.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5'-most exon, compared to variant 1. This variant is represented as non-coding because the use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AA633512, BC070349, BC095436, BM835723, CD176288

Related

ENST00000552039.2