TYMSOS

Summary

TYMSOS (TYMS opposite strand RNA, HGNC:29553) is a long non-coding RNA gene on chromosome 18p11.32.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• GTEx eGene: eQTL in 12 tissues, sQTL in 4 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29553
Approved symbol	TYMSOS
Name	TYMS opposite strand RNA
Location	18p11.32
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000176912
Ensembl biotype	lncRNA
Entrez	494514
RNAcentral	URS00021231D4 — lncRNA, 795 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 lncRNA

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1

ENST00000323813, ENST00000585033, ENST00000664942, ENST00000688530, ENST00000688642, ENST00000701410

RefSeq mRNA: 0

Canonical transcript exons

ENST00000323813 — 2 exons

Exon	Start	End
ENSE00003938205	649473	649964
ENSE00004105405	657842	658352

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 93.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3904 / max 54.1666, expressed in 1191 samples.

Highest expression (Bgee): pancreatic ductal cell, C1 segment of cervical spinal cord, primordial germ cell in gonad, mucosa of transverse colon, putamen.

Genetic regulation across tissues (GTEx eQTL / sQTL)

TYMSOS is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 12 tissues and its splicing (sQTL) in 4 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

16 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Esophagus Muscularis	eqtl	1.6e-24	+0.58	18:667898:T:C
Esophagus Gastroesophageal Junction	eqtl	3.4e-13	+0.54	18:671727:G:A
Cells Cultured fibroblasts	sqtl	2.9e-12	-0.50	18:657443:A:C
Cells Cultured fibroblasts	eqtl	2.4e-11	+0.27	18:656832:T:C
Cells EBV-transformed lymphocytes	eqtl	5.3e-10	+0.39	18:657095:C:T
Cells EBV-transformed lymphocytes	sqtl	1.6e-08	-0.59	18:657352:T:C
Whole Blood	eqtl	5.4e-04	+0.15	18:659236:C:T
Brain Caudate basal ganglia	eqtl	8.7e-04	+0.19	18:651574:T:C
Esophagus Mucosa	eqtl	1.4e-03	-0.24	18:665154:CTT:C
Testis	sqtl	5.4e-03	-1.24	18:419617:C:A
Spleen	eqtl	1.1e-02	-0.80	18:658170:G:T
Artery Aorta	eqtl	1.8e-02	+0.31	18:658064:G:C
Brain Putamen basal ganglia	sqtl	2.3e-02	+0.71	18:658064:G:C
Skin Sun Exposed Lower leg	eqtl	2.6e-02	+0.21	18:658064:G:C
Thyroid	eqtl	3.0e-02	+0.91	18:757274:C:T
Artery Tibial	eqtl	4.6e-02	-0.38	18:335266:C:A

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
170944	3.3904	1191

Top tissues by expression

showing 100 of 246 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	93.23	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	78.47	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.44	gold quality
mucosa of transverse colon	UBERON:0004991	76.82	gold quality
putamen	UBERON:0001874	76.72	gold quality
spinal cord	UBERON:0002240	75.49	gold quality
ventricular zone	UBERON:0003053	74.38	gold quality
amygdala	UBERON:0001876	74.19	gold quality
Brodmann (1909) area 9	UBERON:0013540	73.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.11	silver quality
substantia nigra	UBERON:0002038	71.86	gold quality
Ammon’s horn	UBERON:0001954	71.36	gold quality
ganglionic eminence	UBERON:0004023	70.88	gold quality
hypothalamus	UBERON:0001898	70.12	gold quality
prefrontal cortex	UBERON:0000451	70.08	gold quality
caudate nucleus	UBERON:0001873	70.07	gold quality
midbrain	UBERON:0001891	69.66	gold quality
colonic epithelium	UBERON:0000397	69.64	silver quality
stromal cell of endometrium	CL:0002255	68.28	gold quality
bone marrow cell	CL:0002092	67.17	silver quality
corpus callosum	UBERON:0002336	66.82	gold quality
temporal lobe	UBERON:0001871	66.78	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	66.62	gold quality
tibialis anterior	UBERON:0001385	66.60	silver quality
frontal cortex	UBERON:0001870	66.33	gold quality
right frontal lobe	UBERON:0002810	66.31	gold quality
cerebral cortex	UBERON:0000956	65.84	gold quality
nucleus accumbens	UBERON:0001882	65.58	gold quality
neocortex	UBERON:0001950	65.56	gold quality
forebrain	UBERON:0001890	65.29	gold quality
Brodmann (1909) area 46	UBERON:0006483	65.05	silver quality
ileal mucosa	UBERON:0000331	64.49	silver quality
brain	UBERON:0000955	64.30	gold quality
adult mammalian kidney	UBERON:0000082	63.97	gold quality
anterior cingulate cortex	UBERON:0009835	63.35	gold quality
primary visual cortex	UBERON:0002436	62.95	gold quality
cortex of kidney	UBERON:0001225	62.27	gold quality
bone marrow	UBERON:0002371	61.88	gold quality
cortical plate	UBERON:0005343	61.81	gold quality
rectum	UBERON:0001052	61.80	gold quality
pons	UBERON:0000988	61.47	silver quality
kidney	UBERON:0002113	61.34	gold quality
esophagus mucosa	UBERON:0002469	60.58	gold quality
transverse colon	UBERON:0001157	60.47	gold quality
occipital lobe	UBERON:0002021	59.97	gold quality
right uterine tube	UBERON:0001302	59.92	gold quality
inferior vagus X ganglion	UBERON:0005363	59.56	silver quality
right testis	UBERON:0004534	58.79	gold quality
epithelial cell of pancreas	CL:0000083	58.68	gold quality
duodenum	UBERON:0002114	58.54	gold quality
superior frontal gyrus	UBERON:0002661	58.53	gold quality
esophagus	UBERON:0001043	58.43	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	58.42	gold quality
right hemisphere of cerebellum	UBERON:0014890	58.42	gold quality
left testis	UBERON:0004533	58.36	gold quality
substantia nigra pars reticulata	UBERON:0001966	58.29	gold quality
smooth muscle tissue	UBERON:0001135	58.19	gold quality
deltoid	UBERON:0001476	58.12	gold quality
nasal cavity epithelium	UBERON:0005384	58.00	gold quality
trabecular bone tissue	UBERON:0002483	57.95	gold quality
body of pancreas	UBERON:0001150	57.80	gold quality
postcentral gyrus	UBERON:0002581	57.77	silver quality
upper leg skin	UBERON:0004262	57.64	silver quality
cerebellar cortex	UBERON:0002129	57.44	gold quality
cerebellar hemisphere	UBERON:0002245	57.39	gold quality
gingival epithelium	UBERON:0001949	57.02	gold quality
endothelial cell	CL:0000115	56.85	gold quality
small intestine Peyer’s patch	UBERON:0003454	56.85	gold quality
small intestine	UBERON:0002108	56.78	gold quality
entorhinal cortex	UBERON:0002728	56.75	silver quality
testis	UBERON:0000473	56.72	gold quality
gingiva	UBERON:0001828	56.72	gold quality
kidney epithelium	UBERON:0004819	56.69	gold quality
cerebellum	UBERON:0002037	56.68	gold quality
parietal lobe	UBERON:0001872	56.43	silver quality
lower esophagus	UBERON:0013473	56.24	gold quality
lower esophagus muscularis layer	UBERON:0035833	56.21	gold quality
intestine	UBERON:0000160	56.06	gold quality
adult organism	UBERON:0007023	55.94	silver quality
descending thoracic aorta	UBERON:0002345	55.82	gold quality
large intestine	UBERON:0000059	55.75	gold quality
colon	UBERON:0001155	55.66	gold quality
pancreas	UBERON:0001264	55.55	gold quality
colonic mucosa	UBERON:0000317	55.48	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	55.44	gold quality
tonsil	UBERON:0002372	55.34	gold quality
monocyte	CL:0000576	55.33	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	55.23	gold quality
vermiform appendix	UBERON:0001154	55.14	gold quality
right lobe of liver	UBERON:0001114	55.08	gold quality
parotid gland	UBERON:0001831	55.08	gold quality
liver	UBERON:0002107	54.96	gold quality
mucosa of sigmoid colon	UBERON:0004993	54.96	gold quality
tendon of biceps brachii	UBERON:0008188	54.83	gold quality
anatomical system	UBERON:0000467	54.68	gold quality
multicellular organism	UBERON:0000468	54.40	gold quality
material anatomical entity	UBERON:0000465	54.39	gold quality
thoracic aorta	UBERON:0001515	54.38	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
ascending aorta	UBERON:0001496	54.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.60

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• Positive feedback of SuFu negating protein 1 on Hedgehog signaling promotes colorectal tumor growth. (PMID:33608498)
• Construction of lncRNA TYMSOS/hsa-miR-101-3p/CEP55 and TYMSOS/hsa-miR-195-5p/CHEK1 Axis in Non-small Cell Lung Cancer. (PMID:36352081)
• IncRNA TYMSOS Promotes Epithelial-Mesenchymal Transition and Metastasis in Thyroid Carcinoma through Regulating MARCKSL1 and Activating the PI3K/Akt Signaling Pathway. (PMID:36374807)

Cross-species orthologs

0 orthologs

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CETN1	protein-coding	1068
CLUL1	protein-coding	27098
ENOSF1	protein-coding	55556
TYMS	protein-coding	7298
LINC01925	ncRNA	105376854
YES1	protein-coding	7525

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 38 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

ACEVEDO_LIVER_CANCER_UP, NUYTTEN_EZH2_TARGETS_DN, PEDRIOLI_MIR31_TARGETS_UP, WARTERS_RESPONSE_TO_IR_SKIN, WARTERS_IR_RESPONSE_5GY, ATF6_TARGET_GENES, HMG20B_TARGET_GENES, MAFG_TARGET_GENES, NFKBIA_TARGET_GENES, SETD7_TARGET_GENES, SNRNP70_TARGET_GENES, MIR23A_3P_MIR23B_3P, MIR23C, MIR7856_5P, MIR486_3P, MIR548BA, MIR548AI_MIR570_5P, MIR548AG, MIR6847_5P, MIR4677_3P, MIR5695, BLANCO_MELO_HUMAN_PARAINFLUENZA_VIRUS_3_INFECTION_A594_CELLS_DN, BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_DN, TONG_INTERACT_WITH_PTTG1, JINESH_BLEBBISHIELD_TO_IMMUNE_CELL_FUSION_PBSHMS_UP, JINESH_BLEBBISHIELD_VS_LIVE_CONTROL_UP, DESCARTES_FETAL_ADRENAL_SLC26A4_PAEP_POSITIVE_CELLS, DESCARTES_FETAL_SPLEEN_ERYTHROBLASTS, BRCA2_TARGET_GENES, AEBP2_TARGET_GENES, TET1_TARGET_GENES, NOTCH3_TARGET_GENES, TRAVAGLINI_LUNG_PROLIFERATING_BASAL_CELL, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_1H_UP, chr18p11, PULVER_FOREY_CELLCYCLE_PEAKING_S2, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_UP, FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS

ncRNA interactions

Experimentally supported non-coding-RNA interaction partners (NPInter).

showing 23 of 25 interaction partners:

Partner	Partner type	Level	Source
hsa-miR-619-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-486-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-3150a-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-875-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-452-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-572	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-631	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-483-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
hsa-miR-492	miRNA	RNA-RNA	miRanda with Ago CLIP data GSE52084
DCP1B	protein	RNA-Protein	High-throughput data
hTrmt13	protein	RNA-Protein	High-throughput data
ICP27	protein	RNA-Protein	High-throughput data
IFIT2	protein	RNA-Protein	High-throughput data
KHDRBS2	protein	RNA-Protein	High-throughput data
PARN	protein	RNA-Protein	High-throughput data
TOB1	protein	RNA-Protein	High-throughput data
USF2	protein	RNA-Protein	High-throughput data
SP1	protein	RNA-Protein	High-throughput data
IGF2BP3	protein	RNA-Protein	High-throughput data
SOX2	protein	RNA-Protein	High-throughput data
AGO2	protein	RNA-Protein	High-throughput data
DHX36	protein	RNA-Protein	High-throughput data
miR-4739	miRNA	RNA-RNA	Literature mining

Disease & clinical

ncRNA disease associations

Curated non-coding-RNA → disease associations (LncRNADisease, HMDD) — these are RNA-level associations for this gene, not the positional variant data omitted above.

5 ncRNA–disease associations:

Disease	Causal?	Validated by
Thyroid Neoplasms	Yes	Western Blot, CCK8, qRT-PCR, Flow Cytometry, Luciferase Report Assay, Colony Formation Assay
Carcinoma, Non-Small-Cell Lung	No	Bioinformatics Analysis
Osteosarcoma	No	Western Blot, CCK8, qRT-PCR, Flow Cytometry, RIP, Luciferase Report Assay, Colony Formation Assay, EdU Staining, Transwell Assay
Carcinoma, Non-Small-Cell Lung	Yes	IHC, Transfection, Migration Assay, qRT-PCR, Luciferase Report Assay, Colony Formation Assay
Stomach Neoplasms	Yes	RNA Pull-Down, Flow Cytometry, qRT-PCR, FISH, RIP, Luciferase Report Assay, EdU Staining, Transwell Assay

Drugs & pharmacology

No curated drug or pharmacology associations for this gene.