SCARNA9

Summary

SCARNA9 (small Cajal body-specific RNA 9, HGNC:32566) is a long non-coding RNA gene on chromosome 11q21.

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

Source: NCBI Gene 619383 — RefSeq curated summary.

At a glance

• Gene type: non-coding (lncRNA) — 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:32566
Approved symbol	SCARNA9
Name	small Cajal body-specific RNA 9
Location	11q21
Locus type	RNA, small nucleolar
Status	Approved
Aliases	mgU2-19/30, Z32, lncC11orf54-1
Ensembl gene	ENSG00000254911
Ensembl biotype	lncRNA
Entrez	619383
RNAcentral	URS000075AAF7 — ncRNA, 353 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 lncRNA

ENST00000530422

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000530422 — 1 exons

Exon	Start	End
ENSE00002144202	93721513	93721865

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.2205 / max 2170.9661, expressed in 1281 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116235	5.2205	1281

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	99.68	gold quality
calcaneal tendon	UBERON:0003701	99.07	gold quality
bone marrow cell	CL:0002092	97.68	gold quality
sural nerve	UBERON:0015488	97.39	gold quality
adrenal tissue	UBERON:0018303	97.27	gold quality
bone marrow	UBERON:0002371	94.76	gold quality
corpus callosum	UBERON:0002336	93.91	gold quality
monocyte	CL:0000576	92.07	gold quality
leukocyte	CL:0000738	91.22	gold quality
granulocyte	CL:0000094	90.91	gold quality
tonsil	UBERON:0002372	90.21	gold quality
skeletal muscle tissue	UBERON:0001134	89.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.97	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.12	gold quality
muscle tissue	UBERON:0002385	87.29	gold quality
kidney	UBERON:0002113	85.85	gold quality
primary visual cortex	UBERON:0002436	85.17	gold quality
liver	UBERON:0002107	85.16	gold quality
cortex of kidney	UBERON:0001225	84.80	gold quality
hindlimb stylopod muscle	UBERON:0004252	83.59	gold quality
superior frontal gyrus	UBERON:0002661	83.26	gold quality
stromal cell of endometrium	CL:0002255	82.16	gold quality
endometrium	UBERON:0001295	82.04	gold quality
adult mammalian kidney	UBERON:0000082	81.95	gold quality
blood	UBERON:0000178	81.68	gold quality
mucosa of transverse colon	UBERON:0004991	80.60	gold quality
small intestine	UBERON:0002108	78.29	gold quality
urinary bladder	UBERON:0001255	78.16	gold quality
intestine	UBERON:0000160	78.12	gold quality
spleen	UBERON:0002106	77.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Long non-coding RNA lncC11orf54-1 modulates neuroinflammatory responses by activating NF-kappaB signaling during meningitic Escherichia coli infection. (PMID:34980188)

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.