SCARNA2 Gene

HGNC Family Non-coding RNAs
Name small Cajal body-specific RNA 2
Description Predicted to be involved in RNA processing. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nSCARNA2 is a long noncoding RNA that has been implicated in the clinical behavior of colorectal cancer, where it is highly expressed in tumor tissues relative to adjacent normal tissues. Its overexpression is associated with an unfavorable postoperative prognosis, as SCARNA2 confers chemoresistance by acting as a competing endogenous RNA. In this role, it sequesters miR-342-3p, which in turn facilitates the upregulation of key survival and proliferation factors such as epidermal growth factor receptor (EGFR) and B-cell lymphoma 2 (BCL2) in colorectal cancer cells."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn a distinct functional context, SCARNA2 belongs to the family of C/D box small Cajal body-specific RNAs that guide the site-specific 2′-O-methylation of U2 snRNA, a modification essential for proper splicing. Unlike many other small Cajal body-specific RNAs, SCARNA2 is independently transcribed by RNA polymerase II. Its transcription is regulated by a compact promoter region containing a TATA motif, a binding site for the transcription factor hStaf/ZNF143, and additional conserved promoter elements, underscoring a unique maturation pathway that differs from that of typical mRNAs or snRNAs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nWhile these studies highlight the dual roles of SCARNA2 in modulating chemoresistance and RNA modification processes, its expression pattern and potential functions in other tumor types, such as cutaneous squamous cell carcinoma, remain uncharacterized, indicating an important area for future research."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Peng-Fei Zhang, Jing Wu, Yin Wu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The lncRNA SCARNA2 mediates colorectal cancer chemoresistance through a conserved microRNA-342-3p target sequence."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Physiol (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcp.27684"}], "href": "https://doi.org/10.1002/jcp.27684"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30443961"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30443961"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Marie-Aline Gérard, Evelyne Myslinski, Natassia Chylak, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkp988"}], "href": "https://doi.org/10.1093/nar/gkp988"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19906720"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19906720"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Zhongzhao Zhang, Min Jia, Changhui Wen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Long non-coding RNA SCARNA2 induces cutaneous squamous cell carcinoma progression via modulating miR-342-3p expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Gene Med (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jgm.3242"}], "href": "https://doi.org/10.1002/jgm.3242"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32558970"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32558970"}]}]}]}
Synonyms MGU2-25/61, HBII-382
NCBI Gene ID 677766
API
Download Associations
Predicted Functions View SCARNA2's ARCHS4 Predicted Functions.
Co-expressed Genes View SCARNA2's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View SCARNA2's ARCHS4 Predicted Functions.

Functional Associations

SCARNA2 has 2,573 functional associations with biological entities spanning 6 categories (molecular profile, disease, phenotype or trait, functional term, phrase or reference, chemical, cell line, cell type or tissue, gene, protein or microRNA) extracted from 26 datasets.

Click the + buttons to view associations for SCARNA2 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq tissue samples with high or low expression of SCARNA2 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of SCARNA2 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
CCLE Cell Line Gene Expression Profiles cell lines with high or low expression of SCARNA2 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
CellMarker Gene-Cell Type Associations cell types associated with SCARNA2 gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of SCARNA2 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
ChEA Transcription Factor Targets transcription factors binding the promoter of SCARNA2 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 SCARNA2 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
CTD Gene-Disease Associations diseases associated with SCARNA2 gene/protein from the curated CTD Gene-Disease Associations dataset.
ENCODE Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at SCARNA2 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 SCARNA2 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of SCARNA2 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 SCARNA2 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
GeneRIF Biological Term Annotations biological terms co-occuring with SCARNA2 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
GEO Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of SCARNA2 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 SCARNA2 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 SCARNA2 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 SCARNA2 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 SCARNA2 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 SCARNA2 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 SCARNA2 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 SCARNA2 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 SCARNA2 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles dataset.
KnockTF Gene Expression Profiles with Transcription Factor Perturbations transcription factor perturbations changing expression of SCARNA2 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset.
MotifMap Predicted Transcription Factor Targets transcription factors regulating expression of SCARNA2 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 SCARNA2 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 SCARNA2 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.