SCARNA2

Summary

SCARNA2 (small Cajal body-specific RNA 2, HGNC:32558) is a small Cajal body RNA gene on chromosome 1p13.3.

Predicted to be involved in RNA processing. Predicted to be located in nucleolus.

Source: NCBI Gene 677766 — RefSeq curated summary.

At a glance

• Gene type: non-coding (scaRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32558
Approved symbol	SCARNA2
Name	small Cajal body-specific RNA 2
Location	1p13.3
Locus type	RNA, small nucleolar
Status	Approved
Aliases	mgU2-25/61, HBII-382
Ensembl gene	ENSG00000278249
Ensembl biotype	scaRNA
Entrez	677766
RNAcentral	URS000023DE4C — ncRNA, 420 nt, 2 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 scaRNA

ENST00000458748

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000458748 — 1 exons

Exon	Start	End
ENSE00001807482	109100193	109100612

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 99.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1531.7248 / max 50615.7955, expressed in 1827 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4381	1178.8543	1827
4382	352.8705	1821

Top tissues by expression

131 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	99.75	gold quality
corpus callosum	UBERON:0002336	99.57	gold quality
bone marrow cell	CL:0002092	99.52	gold quality
calcaneal tendon	UBERON:0003701	99.37	gold quality
sural nerve	UBERON:0015488	99.19	gold quality
adrenal tissue	UBERON:0018303	97.54	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.63	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.17	gold quality
tonsil	UBERON:0002372	90.39	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.47	gold quality
superior frontal gyrus	UBERON:0002661	82.96	gold quality
blood	UBERON:0000178	81.91	gold quality
skeletal muscle tissue	UBERON:0001134	81.71	gold quality
bone marrow	UBERON:0002371	81.42	gold quality
primary visual cortex	UBERON:0002436	80.68	gold quality
urinary bladder	UBERON:0001255	80.21	gold quality
kidney	UBERON:0002113	79.93	gold quality
liver	UBERON:0002107	77.76	gold quality
cortex of kidney	UBERON:0001225	77.15	gold quality
uterine cervix	UBERON:0000002	76.91	gold quality
adult mammalian kidney	UBERON:0000082	74.85	gold quality
thoracic mammary gland	UBERON:0005200	74.79	gold quality
mucosa of transverse colon	UBERON:0004991	72.91	gold quality
cortical plate	UBERON:0005343	71.38	gold quality
lung	UBERON:0002048	70.19	gold quality
stomach	UBERON:0000945	70.11	gold quality
ovary	UBERON:0000992	70.06	gold quality
ventricular zone	UBERON:0003053	70.02	gold quality
monocyte	CL:0000576	70.01	gold quality
ganglionic eminence	UBERON:0004023	69.53	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ZNF143

Literature-anchored findings (GeneRIF, showing 4)

• The scaRNA2 gene is transcribed by RNA polymerase II and that the promoter elements responsible for its transcription are contained within a 161 bp region upstream of the transcription start site. (PMID:19906720)
• our results reveal a novel pathway that SCARNA2 regulates colorectal cancer chemoresistance through targeting miR-342-3p-EGFR/BCL2 pathway (PMID:30443961)
• Long non-coding RNA SCARNA2 induces cutaneous squamous cell carcinoma progression via modulating miR-342-3p expression. (PMID:32558970)
• ATR-binding lncRNA ScaRNA2 promotes cancer resistance through facilitating efficient DNA end resection during homologous recombination repair. (PMID:37775817)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.