DIRC3

Summary

DIRC3 (disrupted in renal carcinoma 3, HGNC:17805) is a long non-coding RNA gene on chromosome 2q35.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• GTEx eGene: eQTL in 26 tissues, sQTL in 7 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17805
Approved symbol	DIRC3
Name	disrupted in renal carcinoma 3
Location	2q35
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ14199
Ensembl gene	ENSG00000231672
Ensembl biotype	lncRNA
OMIM	608262
Entrez	729582
RNAcentral	URS0000CCDF88 — lncRNA, 3910 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 15 lncRNA

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 2: 1, TSL 4: 1, TSL 5: 2

ENST00000423123, ENST00000474063, ENST00000484635, ENST00000486365, ENST00000654616, ENST00000663156, ENST00000663562, ENST00000671322, ENST00000675581, ENST00000676082, ENST00000676267, ENST00000717909, ENST00000744938, ENST00000744939, ENST00000832881

RefSeq mRNA: 0

Canonical transcript exons

ENST00000423123 — 5 exons

Exon	Start	End
ENSE00001616462	217739487	217739575
ENSE00001688576	217713029	217713101
ENSE00001762211	217756021	217756147
ENSE00001779758	217703900	217704074
ENSE00004033684	217756468	217756555

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 80.40.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3570 / max 34.9655, expressed in 144 samples.

Highest expression (Bgee): male germ line stem cell (sensu Vertebrata) in testis, layer of synovial tissue, synovial joint, stromal cell of endometrium, coronary artery.

Genetic regulation across tissues (GTEx eQTL / sQTL)

DIRC3 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 26 tissues and its splicing (sQTL) in 7 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 33 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	eqtl	4.6e-32	+0.92	2:217393807:T:C
Artery Tibial	eqtl	1.1e-28	+0.39	2:217799910:T:G
Artery Aorta	eqtl	7.4e-23	+0.40	2:217799910:T:G
Esophagus Muscularis	eqtl	1.3e-19	-0.45	2:217776399:C:A
Colon Sigmoid	eqtl	3.6e-14	+0.42	2:217799910:T:G
Lung	eqtl	2.6e-12	+0.37	2:217772713:C:A
Skin Not Sun Exposed Suprapubic	eqtl	7.8e-11	+0.58	2:217393807:T:C
Esophagus Gastroesophageal Junction	eqtl	3.4e-10	+0.35	2:217799910:T:G
Nerve Tibial	eqtl	5.7e-10	+0.32	2:217772655:G:A
Thyroid	sqtl	5.9e-09	+1.55	2:217415810:A:C
Adipose Subcutaneous	eqtl	6.2e-08	-0.26	2:217764120:T:C
Testis	eqtl	1.7e-07	-0.37	2:217390806:C:T
Testis	sqtl	1.1e-06	+0.45	2:217406996:T:C
Artery Coronary	eqtl	4.5e-06	+0.34	2:217770269:A:G
Colon Transverse	eqtl	2.0e-05	+0.17	2:217795969:A:C
Artery Aorta	sqtl	2.6e-05	-1.89	2:217476883:T:G
Cells EBV-transformed lymphocytes	eqtl	5.3e-05	+0.81	2:217789061:G:A
Artery Tibial	sqtl	6.6e-05	-1.44	2:217433016:A:C
Adipose Visceral Omentum	eqtl	8.8e-05	+0.22	2:217772655:G:A
Esophagus Mucosa	eqtl	8.8e-05	-0.23	2:217419801:C:T

FANTOM5 promoters

6 alternative TSS:

Promoter ID	TPM avg	Samples expressed
33862	0.2170	104
33863	0.0478	31
33856	0.0378	17
33855	0.0374	9
33860	0.0119	1
33854	0.0050	1

Top tissues by expression

showing 100 of 252 tissues 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	80.40	gold quality
layer of synovial tissue	UBERON:0007616	76.59	gold quality
synovial joint	UBERON:0002217	76.48	gold quality
stromal cell of endometrium	CL:0002255	76.41	gold quality
right coronary artery	UBERON:0001625	75.79	gold quality
descending thoracic aorta	UBERON:0002345	75.72	gold quality
thoracic aorta	UBERON:0001515	75.32	gold quality
ascending aorta	UBERON:0001496	75.26	gold quality
popliteal artery	UBERON:0002250	75.10	gold quality
aorta	UBERON:0000947	75.07	gold quality
tibial artery	UBERON:0007610	75.07	gold quality
upper arm skin	UBERON:0004263	73.94	gold quality
right adrenal gland cortex	UBERON:0035827	73.67	gold quality
right adrenal gland	UBERON:0001233	72.32	gold quality
left coronary artery	UBERON:0001626	72.32	gold quality
muscle layer of sigmoid colon	UBERON:0035805	72.32	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	71.68	gold quality
coronary artery	UBERON:0001621	71.66	gold quality
left adrenal gland	UBERON:0001234	71.60	gold quality
smooth muscle tissue	UBERON:0001135	71.58	gold quality
lower esophagus	UBERON:0013473	71.51	gold quality
lower esophagus muscularis layer	UBERON:0035833	71.51	gold quality
left adrenal gland cortex	UBERON:0035825	71.50	gold quality
mucosa of stomach	UBERON:0001199	71.15	gold quality
sural nerve	UBERON:0015488	71.01	gold quality
adrenal gland	UBERON:0002369	70.87	gold quality
adrenal cortex	UBERON:0001235	70.65	gold quality
right lobe of thyroid gland	UBERON:0001119	70.63	gold quality
ventricular zone	UBERON:0003053	70.54	gold quality
left uterine tube	UBERON:0001303	69.84	gold quality
left lobe of thyroid gland	UBERON:0001120	69.74	gold quality
right ovary	UBERON:0002118	69.60	gold quality
left ovary	UBERON:0002119	69.51	gold quality
body of uterus	UBERON:0009853	69.44	gold quality
colonic epithelium	UBERON:0000397	69.29	gold quality
pigmented layer of retina	UBERON:0001782	69.29	gold quality
thyroid gland	UBERON:0002046	68.90	gold quality
ganglionic eminence	UBERON:0004023	68.70	gold quality
adrenal tissue	UBERON:0018303	68.69	gold quality
calcaneal tendon	UBERON:0003701	68.63	gold quality
subcutaneous adipose tissue	UBERON:0002190	68.30	gold quality
myocardium	UBERON:0002349	68.06	gold quality
hindlimb stylopod muscle	UBERON:0004252	67.97	gold quality
cardiac muscle of right atrium	UBERON:0003379	67.80	gold quality
left ventricle myocardium	UBERON:0006566	67.45	gold quality
decidua	UBERON:0002450	67.32	gold quality
adipose tissue	UBERON:0001013	66.80	gold quality
nasal cavity epithelium	UBERON:0005384	66.51	gold quality
myometrium	UBERON:0001296	66.33	gold quality
omental fat pad	UBERON:0010414	66.15	gold quality
peritoneum	UBERON:0002358	66.12	gold quality
adipose tissue of abdominal region	UBERON:0007808	66.01	gold quality
bone marrow cell	CL:0002092	65.86	silver quality
cortical plate	UBERON:0005343	65.71	gold quality
ovary	UBERON:0000992	65.65	gold quality
urinary bladder	UBERON:0001255	65.49	gold quality
esophagus squamous epithelium	UBERON:0006920	65.07	gold quality
kidney epithelium	UBERON:0004819	64.87	gold quality
vermiform appendix	UBERON:0001154	64.73	gold quality
esophagus	UBERON:0001043	64.68	gold quality
trabecular bone tissue	UBERON:0002483	64.05	gold quality
right lung	UBERON:0002167	63.78	gold quality
heart	UBERON:0000948	63.48	gold quality
body of stomach	UBERON:0001161	63.44	gold quality
stomach	UBERON:0000945	63.39	gold quality
bone marrow	UBERON:0002371	63.38	gold quality
heart left ventricle	UBERON:0002084	63.33	gold quality
tendon	UBERON:0000043	63.18	gold quality
cardiac ventricle	UBERON:0002082	63.03	gold quality
gall bladder	UBERON:0002110	62.96	gold quality
colon	UBERON:0001155	62.93	gold quality
large intestine	UBERON:0000059	62.77	gold quality
nucleus accumbens	UBERON:0001882	62.41	gold quality
secondary oocyte	CL:0000655	62.31	gold quality
caecum	UBERON:0001153	62.17	gold quality
intestine	UBERON:0000160	62.08	gold quality
cardiac atrium	UBERON:0002081	61.87	gold quality
tibial nerve	UBERON:0001323	61.74	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	61.68	gold quality
right atrium auricular region	UBERON:0006631	61.66	gold quality
apex of heart	UBERON:0002098	61.62	gold quality
fundus of stomach	UBERON:0001160	61.54	gold quality
transverse colon	UBERON:0001157	61.37	gold quality
spleen	UBERON:0002106	61.33	gold quality
uterus	UBERON:0000995	61.15	gold quality
corpus callosum	UBERON:0002336	61.03	gold quality
right testis	UBERON:0004534	61.03	gold quality
multicellular organism	UBERON:0000468	60.69	gold quality
material anatomical entity	UBERON:0000465	60.68	gold quality
anatomical system	UBERON:0000467	60.61	gold quality
rectum	UBERON:0001052	60.40	gold quality
muscle of leg	UBERON:0001383	60.37	gold quality
small intestine Peyer’s patch	UBERON:0003454	60.35	gold quality
metanephros	UBERON:0000081	60.14	gold quality
lymph node	UBERON:0000029	60.10	gold quality
female reproductive system	UBERON:0000474	59.96	gold quality
small intestine	UBERON:0002108	59.83	gold quality
tonsil	UBERON:0002372	59.83	gold quality
metanephros cortex	UBERON:0010533	59.68	gold quality
postcentral gyrus	UBERON:0002581	59.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.49

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• SNPs rs11903757, with closest proximity to NABP1 and SDPR, and rs966423 in DIRC3, were associated with survival in laryngeal squamous cell carcinoma patients. (PMID:27793000)
• DIRC3 depletion in human melanoma cells leads to increased anchorage-independent growth, a hallmark of malignant transformation, whilst melanoma patients classified by low DIRC3 expression have decreased survival. These results suggest that DIRC3 may be a novel clinically important melanoma tumor suppressor gene. (PMID:31881017)
• lncRNA DIRC3 regulates invasiveness and insulin-like growth factor signaling in thyroid cancer cells. (PMID:37130273)

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
MIR6809	ncRNA	102465485
SNORA115	snoRNA	109623482
TNS1	protein-coding	7145
DIRC3-AS1	ncRNA	105373877
TNS1-AS1	ncRNA	105373878
RUFY4	protein-coding	285180
CXCR2	protein-coding	3579

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 16 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

CIITA_TARGET_GENES, HAND1_TARGET_GENES, ZBTB18_TARGET_GENES, ZNF322_TARGET_GENES, ZNF7_TARGET_GENES, GSE11864_UNTREATED_VS_CSF1_IN_MAC_DN, chr2q35, DESCARTES_MAIN_FETAL_RETINAL_PIGMENT_CELLS, NKX2_5_TARGET_GENES, HARALAMBIEVA_PBMC_M_M_R_II_AGE_11_22YO_VACCINATED_VS_UNVACCINATED_7YR_UP, GSE19198_CTRL_VS_IL21_TREATED_TCELL_6H_DN, GSE36888_UNTREATED_VS_IL2_TREATED_TCELL_17H_UP, GSE41867_DAY6_VS_DAY15_LCMV_CLONE13_EFFECTOR_CD8_TCELL_UP, GSE41867_DAY8_VS_DAY15_LCMV_ARMSTRONG_EFFECTOR_CD8_TCELL_DN, GSE41867_DAY15_EFFECTOR_VS_DAY30_MEMORY_CD8_TCELL_LCMV_ARMSTRONG_DN, GSE46606_UNSTIM_VS_CD40L_IL2_IL5_3DAY_STIMULATED_IRF4_KO_BCELL_UP

ncRNA interactions

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

showing 21 of 23 interaction partners:

Partner	Partner type	Level	Source
ADAR	protein	RNA-Protein	High-throughput data
WDR33	protein	RNA-Protein	High-throughput data
HNRNPA1	protein	RNA-Protein	High-throughput data
HNRNPF	protein	RNA-Protein	High-throughput data
RBM5	protein	RNA-Protein	High-throughput data
RBM6	protein	RNA-Protein	High-throughput data
RBM10	protein	RNA-Protein	High-throughput data
MOV10	protein	RNA-Protein	High-throughput data
UPF1	protein	RNA-Protein	High-throughput data
hnRNPA2B1	protein	RNA-Protein	High-throughput data
FUS	protein	RNA-Protein	High-throughput data
RP11-254F7.1	lncRNA	RNA-RNA	RISE database
TRIM25	protein	RNA-Protein	High-throughput data
ZC3HAV1	protein	RNA-Protein	High-throughput data
ZMAT3	protein	RNA-Protein	High-throughput data
SERBP1	protein	RNA-Protein	High-throughput data
IGF2BP3	protein	RNA-Protein	High-throughput data
SOX2	protein	RNA-Protein	High-throughput data
IGF2BP1	protein	RNA-Protein	High-throughput data
AGO2	protein	RNA-Protein	High-throughput data
DHX36	protein	RNA-Protein	High-throughput data

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.

3 ncRNA–disease associations:

Disease	Causal?	Validated by
Melanoma	No	qRT-PCR, Colony Formation Assay, Western Blot
Atrial Fibrillation	No	RNA-seq
Stomach Neoplasms	No	qRT-PCR, RNA-seq

Drugs & pharmacology

No curated drug or pharmacology associations for this gene.