LINC02913

Summary

LINC02913 (long intergenic non-protein coding RNA 2913, HGNC:31370) is a long non-coding RNA gene on chromosome 9q34.11.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 4 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31370
Approved symbol	LINC02913
Name	long intergenic non-protein coding RNA 2913
Location	9q34.11
Locus type	RNA, long non-coding
Status	Approved
Aliases	bA65J3.5
Ensembl gene	ENSG00000179082
Entrez	414318
RNAcentral	URS0000CCE015 — lncRNA, 843 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, 117 present calls, max score 64.73.

FANTOM5 (CAGE): breadth broad, TPM avg 1.3462 / max 48.7694, expressed in 366 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98901	1.3462	366

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	64.73	silver quality
monocyte	CL:0000576	63.05	gold quality
sural nerve	UBERON:0015488	62.88	gold quality
seminal vesicle	UBERON:0000998	60.19	silver quality
blood	UBERON:0000178	59.77	gold quality
mucosa of stomach	UBERON:0001199	58.99	gold quality
left coronary artery	UBERON:0001626	56.58	gold quality
skin of hip	UBERON:0001554	56.55	silver quality
tibial artery	UBERON:0007610	55.77	gold quality
popliteal artery	UBERON:0002250	55.70	gold quality
coronary artery	UBERON:0001621	55.45	gold quality
ectocervix	UBERON:0012249	54.76	gold quality
ganglionic eminence	UBERON:0004023	54.75	silver quality
descending thoracic aorta	UBERON:0002345	54.72	gold quality
right coronary artery	UBERON:0001625	54.26	gold quality
metanephros cortex	UBERON:0010533	53.90	gold quality
body of stomach	UBERON:0001161	53.67	gold quality
germinal epithelium of ovary	UBERON:0001304	53.60	gold quality
aorta	UBERON:0000947	52.86	gold quality
body of uterus	UBERON:0009853	52.77	gold quality
upper leg skin	UBERON:0004262	52.38	silver quality
stomach	UBERON:0000945	52.35	gold quality
right adrenal gland cortex	UBERON:0035827	52.32	gold quality
uterine cervix	UBERON:0000002	51.83	gold quality
left uterine tube	UBERON:0001303	51.81	gold quality
cortex of kidney	UBERON:0001225	51.76	gold quality
endocervix	UBERON:0000458	51.49	gold quality
smooth muscle tissue	UBERON:0001135	51.03	gold quality
metanephros	UBERON:0000081	50.89	gold quality
blood vessel layer	UBERON:0004797	50.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.91

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Putative uncharacterized protein encoded by LINC02913 — Q8NAJ2 (reviewed: Q8NAJ2)

All UniProt accessions (0):

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

UniProt features (3 total): sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NAJ2-F1	34.66	0.00

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

9 interactions, top by confidence:

A	B	Type	Score
LINC02913	PSMG3	psi-mi:“MI:0915”(physical association)	0.590
PDE9A	LINC02913	psi-mi:“MI:0915”(physical association)	0.560
LINC02913	PSMA3	psi-mi:“MI:0915”(physical association)	0.560
PSMA3	LINC02913	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (4): C9orf106 (Two-hybrid), C9orf106 (Two-hybrid), PSMG3 (Affinity Capture-MS), PSMG3 (Affinity Capture-MS)

ESM2 similar proteins: A8MQB3, A8MWP4, C0HM98, P03400, P0CAT3, P0CZ25, P0DPA3, P58512, P59052, P86434, Q0VFX4, Q3C1V9, Q5SWW7, Q5W150, Q6PRD7, Q6UXR6, Q6UXU0, Q6ZN03, Q6ZR03, Q6ZTC4, Q6ZUF6, Q6ZV77, Q6ZWC4, Q71RG6, Q86UQ8, Q8N1D0, Q8N1V8, Q8N2B8, Q8N2X6, Q8N3U1, Q8N7R1, Q8N8I6, Q8N8Z3, Q8N9P6, Q8N9X3, Q8NAA6, Q8NAJ2, Q8TF63, Q8WXQ3, Q96LS8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
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): RS1000330090 (9:129319707 A>G), RS1000396857 (9:129319471 C>T), RS1000935511 (9:129320712 G>A,T), RS1001066860 (9:129322752 A>G), RS1001801632 (9:129320540 T>A,G), RS1001918784 (9:129322414 A>C,G), RS1002340100 (9:129321665 C>G,T), RS1003870047 (9:129319144 C>T), RS1004875348 (9:129320265 G>C), RS1005108417 (9:129320711 C>A,T), RS1005365036 (9:129320019 T>A,G), RS1005498890 (9:129320949 A>G), RS1005912192 (9:129321197 C>T), RS1007618514 (9:129319456 C>A,T), RS1007649728 (9:129319135 C>A,G,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

2 associations (top):

Study	Trait	p-value
GCST007576_129	Chronotype	3.000000e-11
GCST010732_3	Sensory peripheral neuropathy in microtubule targeting agent-treated breast cancer	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008328	chronotype measurement
EFO:0005260	response to antimicrotubule agent

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
arsenite	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
Air Pollutants, Occupational	affects expression	1
Arsenic	increases methylation	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1

Clinical trials (associated diseases)

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