LINC01033

Summary

LINC01033 (long intergenic non-protein coding RNA 1033, HGNC:49019) is a long non-coding RNA gene on chromosome 5q11.2.

At a glance

• GWAS associations: 16

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:49019
Approved symbol	LINC01033
Name	long intergenic non-protein coding RNA 1033
Location	5q11.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000249069
Entrez	104355136
RNAcentral	URS00002ADE3D — lncRNA, 715 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, 107 present calls, max score 79.79.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.0664 / max 75.6330, expressed in 113 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
56435	0.7269	59
56436	0.3394	92

Top tissues by expression

107 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	79.79	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.24	gold quality
cortical plate	UBERON:0005343	66.26	gold quality
bone marrow	UBERON:0002371	57.64	gold quality
ventricular zone	UBERON:0003053	57.48	silver quality
prefrontal cortex	UBERON:0000451	55.68	gold quality
liver	UBERON:0002107	55.67	gold quality
monocyte	CL:0000576	55.44	gold quality
right lobe of liver	UBERON:0001114	54.18	gold quality
blood	UBERON:0000178	54.14	gold quality
lymph node	UBERON:0000029	53.99	gold quality
superior frontal gyrus	UBERON:0002661	53.79	gold quality
placenta	UBERON:0001987	53.31	gold quality
endometrium	UBERON:0001295	53.00	gold quality
apex of heart	UBERON:0002098	52.26	gold quality
corpus callosum	UBERON:0002336	51.66	gold quality
muscle of leg	UBERON:0001383	51.46	gold quality
gastrocnemius	UBERON:0001388	51.37	gold quality
frontal cortex	UBERON:0001870	50.85	gold quality
islet of Langerhans	UBERON:0000006	50.12	gold quality
heart left ventricle	UBERON:0002084	49.95	gold quality
pancreas	UBERON:0001264	49.83	gold quality
calcaneal tendon	UBERON:0003701	49.20	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	49.07	gold quality
heart	UBERON:0000948	48.36	gold quality
adrenal tissue	UBERON:0018303	48.36	silver quality
smooth muscle tissue	UBERON:0001135	48.18	gold quality
nucleus accumbens	UBERON:0001882	47.18	gold quality
body of pancreas	UBERON:0001150	47.09	gold quality
popliteal artery	UBERON:0002250	47.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.72

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): RS1000035743 (5:54354275 G>A), RS1000062316 (5:54387275 G>A), RS1000133818 (5:54385819 C>T), RS1000168126 (5:54402933 A>T), RS1000197332 (5:54339262 A>G), RS1000238715 (5:54414317 T>C), RS1000239806 (5:54343671 T>A,C), RS1000303665 (5:54344293 A>C), RS1000336881 (5:54367212 C>T), RS1000342820 (5:54376380 A>G), RS1000388038 (5:54349957 G>A,T), RS1000431435 (5:54380509 C>A), RS1000465493 (5:54391852 G>T), RS1000539054 (5:54398682 G>A), RS1000544835 (5:54340211 T>C)

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

16 associations (top):

Study	Trait	p-value
GCST004611_124	High light scatter reticulocyte count	1.000000e-11
GCST004612_70	High light scatter reticulocyte percentage of red cells	4.000000e-11
GCST004619_137	Reticulocyte fraction of red cells	5.000000e-11
GCST004619_34	Reticulocyte fraction of red cells	2.000000e-12
GCST004622_175	Reticulocyte count	4.000000e-13
GCST004622_176	Reticulocyte count	2.000000e-12
GCST90002385_278	High light scatter reticulocyte count	4.000000e-35
GCST90002385_279	High light scatter reticulocyte count	2.000000e-25
GCST90002386_48	High light scatter reticulocyte percentage of red cells	6.000000e-33
GCST90002386_49	High light scatter reticulocyte percentage of red cells	1.000000e-23
GCST90002404_201	Red cell distribution width	6.000000e-14
GCST90002404_225	Red cell distribution width	4.000000e-22
GCST90002405_60	Reticulocyte count	2.000000e-39
GCST90002405_61	Reticulocyte count	6.000000e-29
GCST90002406_168	Reticulocyte fraction of red cells	1.000000e-36
GCST90002406_169	Reticulocyte fraction of red cells	4.000000e-25

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1

Clinical trials (associated diseases)

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