SNORA31 Gene

HGNC Family Non-coding RNAs
Name small nucleolar RNA, H/ACA box 31
Description Predicted to be involved in RNA processing. Predicted to be located in nucleolus. Implicated in brain disease. [provided by Alliance of Genome Resources, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nSNORA31 is a small nucleolar RNA of the H/ACA class that guides the pseudouridylation of uridine residues in small nuclear and ribosomal RNAs, and it plays a unique role in central nervous system immunity. Studies have shown that heterozygous rare variants of SNORA31 impair neuron‐intrinsic antiviral responses, as evidenced by human pluripotent stem cell–derived cortical neurons becoming susceptible to herpes simplex virus-1 (HSV-1) infection. Notably, while these neurons retain normal responses to TLR3 and interferon‑α/β stimulation, their specific abnormal response to HSV-1 suggests that SNORA31 orchestrates an unconventional antiviral immune mechanism in the forebrain, which can be partially rescued by exogenous interferon‑β."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "In complementary studies examining neuronal regulatory proteins, research on Caskin1—a synaptic adaptor binding partner of CASK—has revealed its broad distribution throughout the brain and spinal cord, primarily at synaptic sites. Knockout models have demonstrated that the absence of Caskin1 leads to alterations in gait, enhanced nociception, anxiety-like behavior, and deficits in contextual and cued fear conditioning, highlighting its importance in modulating various behavioral phenotypes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "Further investigations into related neuronal scaffold proteins, Caskin1 and Caskin2, have connected these molecules to postsynaptic structure and function. Deletion of both Caskins results in notable deficits in novelty recognition and spatial memory, along with ultrastructural changes in hippocampal synapses and altered AMPA receptor phosphorylation, underscoring their role in synaptic plasticity and memory formation. These findings stand in contrast to the immunomodulatory function of SNORA31, delineating distinct molecular pathways that support neuronal integrity and function."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Fabien G Lafaille, Oliver Harschnitz, Yoon Seung Lee, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Human SNORA31 variations impair cortical neuron-intrinsic immunity to HSV-1 and underlie herpes simplex encephalitis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Med (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41591-019-0672-3"}], "href": "https://doi.org/10.1038/s41591-019-0672-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31806906"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31806906"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Tayo Katano, Keizo Takao, Manabu Abe, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Distribution of Caskin1 protein and phenotypic characterization of its knockout mice using a comprehensive behavioral test battery."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Brain (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s13041-018-0407-2"}], "href": "https://doi.org/10.1186/s13041-018-0407-2"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30359304"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30359304"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Norbert Bencsik, Szilvia Pusztai, Sándor Borbély, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Dendritic spine morphology and memory formation depend on postsynaptic Caskin proteins."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41598-019-53317-9"}], "href": "https://doi.org/10.1038/s41598-019-53317-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31727973"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31727973"}]}]}]}
Synonyms ACA31, SNORA31A
NCBI Gene ID 677814
API
Download Associations
Predicted Functions View SNORA31's ARCHS4 Predicted Functions.
Co-expressed Genes View SNORA31's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View SNORA31's ARCHS4 Predicted Functions.

Functional Associations

SNORA31 has 1,611 functional associations with biological entities spanning 5 categories (molecular profile, functional term, phrase or reference, chemical, cell line, cell type or tissue, gene, protein or microRNA) extracted from 18 datasets.

Click the + buttons to view associations for SNORA31 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of SNORA31 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
ChEA Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of SNORA31 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
ChEA Transcription Factor Targets transcription factors binding the promoter of SNORA31 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
COSMIC Cell Line Gene CNV Profiles cell lines with high or low copy number of SNORA31 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
ENCODE Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at SNORA31 gene from the ENCODE Histone Modification Site Profiles dataset.
ENCODE Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of SNORA31 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of SNORA31 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
ESCAPE Omics Signatures of Genes and Proteins for Stem Cells PubMedIDs of publications reporting gene signatures containing SNORA31 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
GeneSigDB Published Gene Signatures PubMedIDs of publications reporting gene signatures containing SNORA31 from the GeneSigDB Published Gene Signatures dataset.
GEO Signatures of Differentially Expressed Genes for Small Molecules small molecule perturbations changing expression of SNORA31 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
GTEx Tissue Gene Expression Profiles tissues with high or low expression of SNORA31 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
GTEx Tissue Sample Gene Expression Profiles tissue samples with high or low expression of SNORA31 gene relative to other tissue samples from the GTEx Tissue Sample Gene Expression Profiles dataset.
JASPAR Predicted Transcription Factor Targets transcription factors regulating expression of SNORA31 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles cell lines with high or low copy number of SNORA31 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles cell lines with high or low expression of SNORA31 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles dataset.
MotifMap Predicted Transcription Factor Targets transcription factors regulating expression of SNORA31 gene predicted using known transcription factor binding site motifs from the MotifMap Predicted Transcription Factor Targets dataset.
Roadmap Epigenomics Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at SNORA31 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset.
TCGA Signatures of Differentially Expressed Genes for Tumors tissue samples with high or low expression of SNORA31 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.