SCARNA1 Gene

HGNC Family Non-coding RNAs
Name small Cajal body-specific RNA 1
Description Predicted to be involved in RNA processing. Predicted to be located in Cajal body and nucleolus. [provided by Alliance of Genome Resources, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nThe two provided abstracts focus primarily on the functional characterization of protein‐coding genes involved in neurological and circadian regulation. Specifically, one study identified a novel gene (Nmf9) whose mutations yield vestibular, learning, and circadian deficits across species"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ", while the other systematically mapped the expression of the mWAKE gene across diverse brain regions with implications for arousal timing."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " Neither investigation, however, directly addressed the functional role of SCARNA1.\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nSCARNA1 is categorized as a small Cajal body‐specific RNA known in other contexts to participate in the post‐transcriptional modification of spliceosomal small nuclear RNAs. Despite its importance in RNA biogenesis and modification, the abstracts at hand concentrate on protein-coding genes and their influence on neuronal circuits and behaviors, leaving the possible contributions or mechanistic details of SCARNA1 unexamined.\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn summary, while the studies provide valuable insights into gene functions that affect neurological and circadian processes, they do not elaborate on any role for SCARNA1. Future research addressing noncoding RNAs like SCARNA1 may illuminate additional layers of regulation in neural function and signal transduction that complement the protein-centric mechanisms characterized in these works."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Shuxiao Zhang, Kevin D Ross, Glen A Seidner, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS Genet (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pgen.1005344"}], "href": "https://doi.org/10.1371/journal.pgen.1005344"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26131556"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26131556"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Benjamin J Bell, Annette A Wang, Dong Won Kim, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Characterization of mWake expression in the murine brain."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Comp Neurol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/cne.25066"}], "href": "https://doi.org/10.1002/cne.25066"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33140455"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33140455"}]}]}]}
Synonyms ACA35
NCBI Gene ID 677774
API
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Predicted Functions View SCARNA1's ARCHS4 Predicted Functions.
Co-expressed Genes View SCARNA1's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View SCARNA1's ARCHS4 Predicted Functions.

Functional Associations

SCARNA1 has 501 functional associations with biological entities spanning 4 categories (molecular profile, chemical, cell line, cell type or tissue, gene, protein or microRNA) extracted from 18 datasets.

Click the + buttons to view associations for SCARNA1 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 SCARNA1 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 SCARNA1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
ChEA Transcription Factor Targets transcription factors binding the promoter of SCARNA1 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 SCARNA1 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 SCARNA1 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 SCARNA1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of SCARNA1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
GEO Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of SCARNA1 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Kinase Perturbations kinase perturbations changing expression of SCARNA1 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Small Molecules small molecule perturbations changing expression of SCARNA1 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations transcription factor perturbations changing expression of SCARNA1 gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset.
GTEx Tissue Gene Expression Profiles tissues with high or low expression of SCARNA1 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
JASPAR Predicted Transcription Factor Targets transcription factors regulating expression of SCARNA1 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 SCARNA1 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
KnockTF Gene Expression Profiles with Transcription Factor Perturbations transcription factor perturbations changing expression of SCARNA1 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset.
MotifMap Predicted Transcription Factor Targets transcription factors regulating expression of SCARNA1 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 SCARNA1 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 SCARNA1 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.