LINC03040

Summary

LINC03040 (long intergenic non-protein coding RNA 3040, HGNC:28692) is a protein-coding gene on chromosome 6p21.1, encoding Uncharacterized protein LINC03040 (Q8N319).

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 6 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28692
Approved symbol	LINC03040
Name	long intergenic non-protein coding RNA 3040
Location	6p21.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	MGC45491
Ensembl gene	ENSG00000181577
Ensembl biotype	protein_coding
Entrez	221416
RNAcentral	URS0000E60A9E — lncRNA, 5250 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000336600, ENST00000439969, ENST00000442114, ENST00000448947

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000336600 — 4 exons

Exon	Start	End
ENSE00002046008	44002681	44007612
ENSE00002207843	44000585	44000700
ENSE00002222523	44001017	44001143
ENSE00004034795	44002053	44002127

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 84.20.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5768 / max 85.0571, expressed in 298 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
67945	1.4451	286
67946	0.1317	66

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	84.20	silver quality
endothelial cell	CL:0000115	81.54	gold quality
lower lobe of lung	UBERON:0008949	80.45	silver quality
pigmented layer of retina	UBERON:0001782	79.86	gold quality
cerebellar vermis	UBERON:0004720	79.80	gold quality
tibialis anterior	UBERON:0001385	78.42	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	77.09	silver quality
ileal mucosa	UBERON:0000331	77.07	silver quality
upper arm skin	UBERON:0004263	76.40	gold quality
cardia of stomach	UBERON:0001162	75.80	silver quality
epithelial cell of pancreas	CL:0000083	74.87	gold quality
vena cava	UBERON:0004087	74.50	gold quality
body of tongue	UBERON:0011876	74.00	silver quality
nipple	UBERON:0002030	73.86	silver quality
thymus	UBERON:0002370	73.56	silver quality
layer of synovial tissue	UBERON:0007616	73.04	silver quality
pericardium	UBERON:0002407	72.86	gold quality
dorsal root ganglion	UBERON:0000044	72.79	silver quality
lateral globus pallidus	UBERON:0002476	72.67	gold quality
pons	UBERON:0000988	72.55	gold quality
germinal epithelium of ovary	UBERON:0001304	72.55	gold quality
substantia nigra pars reticulata	UBERON:0001966	72.54	gold quality
epithelium of nasopharynx	UBERON:0001951	72.46	gold quality
lateral nuclear group of thalamus	UBERON:0002736	72.43	gold quality
superior vestibular nucleus	UBERON:0007227	72.18	silver quality
renal medulla	UBERON:0000362	72.13	silver quality
gingival epithelium	UBERON:0001949	71.84	gold quality
substantia nigra pars compacta	UBERON:0001965	71.53	gold quality
synovial joint	UBERON:0002217	70.66	silver quality
gingiva	UBERON:0001828	70.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.06

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Uncharacterized protein LINC03040 — Q8N319 (reviewed: Q8N319)

All UniProt accessions (1): Q8N319

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N319-3	1	yes
Q8N319-4	2

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR041009	DUF5550	Family

Pfam: PF17704

UniProt features (10 total): compositionally biased region 3, region of interest 2, sequence variant 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N319-F1	49.90	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): GGGTGGRR_PAX4_03, SREBP1_02, RGAGGAARY_PU1_Q6, ETS_Q4, MMEF2_Q6, SREBP1_Q6, SREBP_Q3, E2F2_TARGET_GENES, LHX9_TARGET_GENES, MAML1_TARGET_GENES, MIR4728_5P, MIR33A_3P, MIR4516, MIR4441, MIR6127

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

162 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LINC03040	KCNV2	Q8TDN2	575
LINC03040	PTGR3	Q8N4Q0	543
LINC03040	TDRP	Q86YL5	434
LINC03040	ZNF700	Q9H0M5	411
LINC03040	KRTAP5-7	Q6L8G8	407
LINC03040	ZFPM2	Q8WW38	402
LINC03040	MRPL14	Q6P1L8	398
LINC03040	OR1J1	Q8NGS3	397
LINC03040	FGD6	Q6ZV73	371
LINC03040	TMEM63B	Q5T3F8	370
LINC03040	BLTP3B	A0JNW5	370
LINC03040	TEDC2	Q7L2K0	369
LINC03040	NT5DC1	Q5TFE4	357
LINC03040	STON1	Q9Y6Q2	352
LINC03040	TMEM171	Q8WVE6	311

IntAct

0 interactions, top by confidence:

BioGRID (2): C6orf223 (Affinity Capture-RNA), C6orf223 (Two-hybrid)

ESM2 similar proteins: A0A1W2PPE3, A0A3B3IS91, A0A6I8MX38, A0A6I8PU40, A8MTW9, B1AH88, B3EWF7, C0HLS1, C0HMD6, H3BQW9, I3L0S3, I3L1E1, O70738, O75638, P03289, P0C880, P0DI83, P11300, P13985, P16807, P29164, P33485, P59091, P80612, Q01480, Q01900, Q3SYB3, Q5JLA7, Q5SY85, Q5T4H9, Q63003, Q6EEV4, Q6VB84, Q86SI9, Q8N1I8, Q8N1X5, Q8N319, Q8N6K4, Q8N6U2, Q8N726

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

6 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

530 predictions. Top by Δscore:

Variant	Effect	Δscore
6:44000699:GG:G	donor_gain	0.9900
6:44000700:GG:G	donor_gain	0.9900
6:44002679:A:AG	acceptor_gain	0.9900
6:44002680:G:GG	acceptor_gain	0.9900
6:44000697:GAGG:G	donor_gain	0.9800
6:44000698:AGG:A	donor_loss	0.9800
6:44000699:GGGTG:G	donor_loss	0.9800
6:44000700:GGT:G	donor_loss	0.9800
6:44000702:T:G	donor_loss	0.9800
6:44000657:G:GT	donor_gain	0.9700
6:44000696:GGAGG:G	donor_gain	0.9700
6:44000697:GAGGG:G	donor_gain	0.9700
6:44000703:G:GG	donor_loss	0.9700
6:44000698:A:T	donor_gain	0.9600
6:44002680:GTC:G	acceptor_gain	0.9600
6:44000660:G:GT	donor_gain	0.9500
6:44002680:GT:G	acceptor_gain	0.9500
6:44002680:GTCC:G	acceptor_gain	0.9500
6:44002680:GTCCA:G	acceptor_gain	0.9500
6:44000676:G:GT	donor_gain	0.9400
6:44000701:G:GG	donor_gain	0.9400
6:44002121:A:T	donor_gain	0.9400
6:44000705:G:C	donor_loss	0.9300
6:44000817:GCCC:G	donor_gain	0.9300
6:44002052:GATCT:G	acceptor_gain	0.9300
6:44002123:AGCAG:A	donor_loss	0.9300
6:44002125:CAG:C	donor_loss	0.9300
6:44002126:AGG:A	donor_loss	0.9300
6:44002127:G:GT	donor_loss	0.9300
6:44002128:GTA:G	donor_loss	0.9300

AlphaMissense

1500 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:44002959:T:C	F188L	0.953
6:44002961:C:A	F188L	0.953
6:44002961:C:G	F188L	0.953
6:44003066:T:A	N223K	0.888
6:44003066:T:G	N223K	0.888
6:44000682:G:C	W21C	0.871
6:44000682:G:T	W21C	0.871
6:44000624:T:C	M2T	0.869
6:44003030:T:A	N211K	0.860
6:44003030:T:G	N211K	0.860
6:44000625:G:A	M2I	0.825
6:44000625:G:C	M2I	0.825
6:44000625:G:T	M2I	0.825
6:44002960:T:C	F188S	0.808
6:44002818:T:C	F141L	0.800
6:44002820:C:A	F141L	0.800
6:44002820:C:G	F141L	0.800
6:44002960:T:G	F188C	0.794
6:44002715:G:C	W106C	0.785
6:44002715:G:T	W106C	0.785
6:44003029:A:T	N211I	0.784
6:44003043:G:T	G216W	0.763
6:44003057:G:A	M220I	0.752
6:44003057:G:C	M220I	0.752
6:44003057:G:T	M220I	0.752
6:44000680:T:A	W21R	0.749
6:44000680:T:C	W21R	0.749
6:44003067:T:C	Y224H	0.743
6:44000624:T:G	M2R	0.736
6:44003027:A:C	R210S	0.734

dbSNP variants (sampled 300 via entrez): RS1000045326 (6:44000362 G>A), RS1000111831 (6:44005347 T>C), RS1000219982 (6:43999966 A>T), RS1000240414 (6:44005003 T>A), RS1001516579 (6:44001212 T>G), RS1001662442 (6:44005654 A>C), RS1001776960 (6:44006002 C>T), RS1002112337 (6:44004735 C>G), RS1002400788 (6:44004004 TG>T), RS1002451755 (6:44004213 T>A), RS1002665133 (6:44006950 A>T), RS1002774621 (6:44007154 C>G), RS1002865244 (6:44006825 CCA>C), RS1003866910 (6:44005500 G>A), RS1003919148 (6:44005759 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

15 associations (top):

Study	Trait	p-value
GCST001155_1	Vascular endothelial growth factor levels	0.000000e+00
GCST001155_4	Vascular endothelial growth factor levels	2.000000e-26
GCST002766_2	Exudative age-related macular degeneration	6.000000e-18
GCST002863_1	Behavioral disturbance or psychiatric symptoms in prion disease	8.000000e-06
GCST003403_4	Vascular endothelial growth factor levels	4.000000e-17
GCST003988_17	Hypothyroidism	5.000000e-10
GCST005956_58	Waist-to-hip ratio adjusted for BMI	7.000000e-26
GCST005957_1	Waist-to-hip ratio adjusted for BMI (age <50)	2.000000e-14
GCST005958_2	Waist-to-hip ratio adjusted for BMI (age >50)	2.000000e-19
GCST005962_2	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	3.000000e-31
GCST009144_30	Disease progression in age-related macular degeneration (adjusted for baseline)	9.000000e-07
GCST90000584_10	Inflammatory biomarkers (multivariate analysis)	1.000000e-11
GCST90000584_9	Inflammatory biomarkers (multivariate analysis)	3.000000e-296
GCST90011898_144	Alanine aminotransferase levels	4.000000e-14
GCST90011899_78	Aspartate aminotransferase levels	1.000000e-16

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0008336	disease progression measurement
EFO:0004872	inflammatory biomarker measurement
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sotorasib	affects cotreatment, decreases expression	1
perfluorooctanoic acid	increases expression	1
hydroquinone	increases expression	1
2-palmitoylglycerol	increases expression	1
K 7174	decreases expression	1
licochalcone B	decreases expression	1
trametinib	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Zoledronic Acid	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	increases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1
Permethrin	increases expression	1

Clinical trials (associated diseases)

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