SMIM2-IT1

Summary

SMIM2-IT1 (SMIM2 intronic transcript 1, HGNC:41492) is a long non-coding RNA gene on chromosome 13q14.11.

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41492
Approved symbol	SMIM2-IT1
Name	SMIM2 intronic transcript 1
Location	13q14.11
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000235285
Entrez	100874377
RNAcentral	URS000017F86B — lncRNA, 478 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 108 present calls, max score 92.13.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.13	gold quality
left testis	UBERON:0004533	75.85	gold quality
right testis	UBERON:0004534	75.31	gold quality
testis	UBERON:0000473	75.10	gold quality
skeletal muscle tissue	UBERON:0001134	70.86	gold quality
hindlimb stylopod muscle	UBERON:0004252	70.33	gold quality
muscle of leg	UBERON:0001383	66.44	gold quality
gastrocnemius	UBERON:0001388	66.04	gold quality
sural nerve	UBERON:0015488	65.06	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	64.06	gold quality
prefrontal cortex	UBERON:0000451	59.08	gold quality
rectum	UBERON:0001052	56.56	gold quality
superior frontal gyrus	UBERON:0002661	55.97	gold quality
duodenum	UBERON:0002114	55.67	gold quality
islet of Langerhans	UBERON:0000006	55.31	gold quality
vermiform appendix	UBERON:0001154	55.09	gold quality
tibial artery	UBERON:0007610	55.00	gold quality
popliteal artery	UBERON:0002250	54.97	gold quality
primary visual cortex	UBERON:0002436	54.07	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	53.35	gold quality
frontal cortex	UBERON:0001870	53.09	gold quality
monocyte	CL:0000576	52.57	silver quality
multicellular organism	UBERON:0000468	52.28	gold quality
blood	UBERON:0000178	51.87	gold quality
calcaneal tendon	UBERON:0003701	51.28	silver quality
kidney	UBERON:0002113	50.83	gold quality
adult mammalian kidney	UBERON:0000082	50.70	gold quality
fundus of stomach	UBERON:0001160	50.46	gold quality
cerebral cortex	UBERON:0000956	50.06	gold quality
left uterine tube	UBERON:0001303	49.38	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.97

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (0):

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000463019 (13:44155442 T>C), RS1000797890 (13:44150470 C>A,G), RS1000829921 (13:44159899 C>G), RS1001007641 (13:44152635 T>A), RS1001350159 (13:44157266 C>T), RS1001737581 (13:44159479 C>A), RS1002011720 (13:44150053 C>T), RS1002127726 (13:44149733 C>T), RS1002379611 (13:44146691 C>T), RS1002632758 (13:44153427 G>A,C), RS1002704746 (13:44156039 A>G), RS1002727211 (13:44153865 G>A,T), RS1002823383 (13:44146543 G>A), RS1002916496 (13:44154949 T>C), RS1003079405 (13:44146909 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.