RNU1-1

Summary

RNU1-1 (RNA, U1 small nuclear 1, HGNC:10120) is a small nuclear RNA gene on chromosome 1p36.13.

Predicted to enable pre-mRNA 5’-splice site binding activity. Predicted to be involved in mRNA 5’-splice site recognition. Predicted to be part of U1 snRNP.

Source: NCBI Gene 26871 — RefSeq curated summary.

At a glance

• Gene type: non-coding (snRNA) — 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:10120
Approved symbol	RNU1-1
Name	RNA, U1 small nuclear 1
Location	1p36.13
Locus type	RNA, small nuclear
Status	Approved
Aliases	Rnu1a1, U1, HU1-1, U1A1, HSD1
Ensembl gene	ENSG00000206652
Ensembl biotype	snRNA
Entrez	26871
RNAcentral	URS0002A146BA — snRNA, 168 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 snRNA

ENST00000383925

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000383925 — 1 exons

Exon	Start	End
ENSE00001808303	16514122	16514285

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 99.96.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1538 / max 54.1666, expressed in 46 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
10540	0.1538	46

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	99.96	gold quality
adrenal tissue	UBERON:0018303	99.95	gold quality
sural nerve	UBERON:0015488	99.92	gold quality
calcaneal tendon	UBERON:0003701	99.76	gold quality
granulocyte	CL:0000094	96.26	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.57	gold quality
bone marrow	UBERON:0002371	86.35	gold quality
blood	UBERON:0000178	86.21	gold quality
monocyte	CL:0000576	85.95	gold quality
leukocyte	CL:0000738	85.84	gold quality
skeletal muscle tissue	UBERON:0001134	80.18	gold quality
left testis	UBERON:0004533	79.76	gold quality
testis	UBERON:0000473	79.29	gold quality
right testis	UBERON:0004534	79.05	gold quality
putamen	UBERON:0001874	78.91	gold quality
liver	UBERON:0002107	78.34	gold quality
cerebellar hemisphere	UBERON:0002245	77.79	gold quality
cerebellar cortex	UBERON:0002129	77.28	gold quality
caudate nucleus	UBERON:0001873	77.26	gold quality
cerebellum	UBERON:0002037	77.15	gold quality
muscle of leg	UBERON:0001383	76.48	gold quality
nucleus accumbens	UBERON:0001882	76.32	gold quality
gastrocnemius	UBERON:0001388	75.99	gold quality
anterior cingulate cortex	UBERON:0009835	75.25	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.22	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.10	gold quality
brain	UBERON:0000955	74.80	gold quality
amygdala	UBERON:0001876	74.39	gold quality
Ammon’s horn	UBERON:0001954	73.96	gold quality
subcutaneous adipose tissue	UBERON:0002190	73.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.93

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ETV7, SPDEF, TBP, TP53, VSX1

Literature-anchored findings (GeneRIF, showing 9)

• U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression (PMID:21362553)
• Authors propose that U1 shortage causes transcript shortening because, as cotranscriptional recruitment of U1 to nascent transcripts becomes limiting, it leaves distal polyadenylation signals less protected, providing a built-in and U1 dose-dependent mechanism for mRNA length regulation and isoform switching. (PMID:22770214)
• Human U1 snRNA variants are unable to efficiently bind U1 snRNP proteins. (PMID:24583175)
• An imbalance in the vU1/U1 ratio, rather than an overall reduction in Uridyl-rich (U)-snRNAs, may contribute to the specific neuromuscular disease phenotype associated with spinal muscular atrophy. (PMID:27536002)
• We found that only the modified U1 snRNA (IVS-AAA) that completely matched both the intronic and exonic U1 binding sequences of the mutated DDC gene could correct splicing errors of either the mutated human DDC minigene or the mouse artificial splicing construct in vitro (PMID:27658936)
• The authors show that U1 telescripting is selectively required for sustaining long-distance transcription elongation in introns of large genes (median 39 kb). (PMID:28967884)
• Structural insights into recognition of SL4, the UUCG stem-loop, of human U1 snRNA by the ubiquitin-like domain, including the C-terminal tail in the SF3A1 subunit of U2 snRNP. (PMID:37094335)
• Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing. (PMID:38164604)
• Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs. (PMID:38426935)

Cross-species orthologs

0 orthologs

Paralogs (147): RNU1-75P (ENSG00000194297), RNU1-15P (ENSG00000195024), RNU1-58P (ENSG00000199283), RNU1-150P (ENSG00000199361), RNU1-108P (ENSG00000199426), RNU1-62P (ENSG00000199469), RNU1-70P (ENSG00000199488), RNU1-94P (ENSG00000199497), RNU1-14P (ENSG00000199629), RNU1-35P (ENSG00000199652), RNU1-38P (ENSG00000199687), RNU1-76P (ENSG00000199773), RNU1-134P (ENSG00000199805), RNU1-47P (ENSG00000199836), RNU1-72P (ENSG00000199846), RNVU1-22 (ENSG00000199879), RNU1-17P (ENSG00000199892), RNU1-18P (ENSG00000199932), RNU1-19P (ENSG00000200176), RNU1-20P (ENSG00000200184), RNU1-21P (ENSG00000200197), RNU1-22P (ENSG00000200204), RNU1-23P (ENSG00000200231), RNU1-83P (ENSG00000200296), RNU1-49P (ENSG00000200338), RNU1-105P (ENSG00000200340), RNVU1-33 (ENSG00000200597), RNU1-124P (ENSG00000200731), RNU1-31P (ENSG00000200745), RNU1-65P (ENSG00000200789), RNU1-130P (ENSG00000200800), RNU1-32P (ENSG00000200807), RNU1-146P (ENSG00000200885), RNU1-42P (ENSG00000200903), RNU1-7P (ENSG00000200975), RNVU1-34 (ENSG00000200997), RNU1-96P (ENSG00000201033), RNU1-33P (ENSG00000201119), RNU1-151P (ENSG00000201142), RNU1-24P (ENSG00000201155)

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.