PIK3CD-AS2

Summary

PIK3CD-AS2 (PIK3CD antisense RNA 2, HGNC:51334) is a long non-coding RNA gene on chromosome 1p36.22.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to PIK3CD — the sense gene carries 9 GWAS associations, 66 ChEMBL molecules (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 16 tissues, sQTL in 10 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51334
Approved symbol	PIK3CD-AS2
Name	PIK3CD antisense RNA 2
Location	1p36.22
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000231789
Ensembl biotype	lncRNA
Entrez	101929074
RNAcentral	URS00007E3AB7 — lncRNA, 958 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 lncRNA

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

ENST00000415330, ENST00000775830, ENST00000775831

RefSeq mRNA: 0

Canonical transcript exons

ENST00000415330 — 3 exons

Exon	Start	End
ENSE00003455420	9672405	9672719
ENSE00003987853	9680712	9681135
ENSE00004143074	9687335	9687604

Expression profiles

Bgee: expression breadth ubiquitous, 152 present calls, max score 85.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.4703 / max 59.4981, expressed in 1150 samples.

Highest expression (Bgee): primordial germ cell in gonad, sural nerve, olfactory segment of nasal mucosa, stromal cell of endometrium, colonic epithelium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PIK3CD-AS2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 16 tissues and its splicing (sQTL) in 10 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 26 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Thyroid	eqtl	5.6e-21	-0.30	1:9681734:A:G
Thyroid	sqtl	4.5e-19	+0.56	1:9681654:C:G
Cells EBV-transformed lymphocytes	sqtl	1.4e-13	-0.69	1:9681734:A:G
Colon Sigmoid	eqtl	2.2e-10	+1.10	1:9687685:C:T
Esophagus Muscularis	eqtl	6.1e-10	+0.96	1:9687685:C:T
Artery Tibial	eqtl	1.6e-08	+0.81	1:9687685:C:T
Pancreas	sqtl	8.4e-08	+0.56	1:9683176:T:C
Nerve Tibial	eqtl	1.1e-07	+0.77	1:9687685:C:T
Esophagus Gastroesophageal Junction	eqtl	2.6e-06	+0.86	1:9687685:C:T
Cells Cultured fibroblasts	sqtl	2.0e-04	-0.33	1:9683176:T:C
Artery Aorta	eqtl	5.0e-04	+0.76	1:9687685:C:T
Brain Anterior cingulate cortex BA24	eqtl	7.6e-04	+1.17	1:9683768:A:T
Heart Atrial Appendage	eqtl	1.6e-03	+0.65	1:9687685:C:T
Cells EBV-transformed lymphocytes	eqtl	4.8e-03	-0.53	1:9673908:A:G
Kidney Cortex	sqtl	7.2e-03	-0.83	1:9679377:T:C
Artery Coronary	eqtl	7.6e-03	+0.93	1:9687685:C:T
Breast Mammary Tissue	sqtl	9.3e-03	-0.31	1:9686554:G:A
Adipose Visceral Omentum	eqtl	9.5e-03	+0.44	1:9687685:C:T
Brain Nucleus accumbens basal ganglia	eqtl	1.1e-02	+1.04	1:10087001:GC:G
Ovary	sqtl	2.1e-02	+0.53	1:9690768:G:T

FANTOM5 promoters

5 alternative TSS:

Promoter ID	TPM avg	Samples expressed
10228	4.7172	1070
10226	0.3566	241
10225	0.1921	90
10227	0.1259	52
10224	0.0786	17

Top tissues by expression

showing 100 of 244 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.10	gold quality
sural nerve	UBERON:0015488	72.68	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	72.01	gold quality
stromal cell of endometrium	CL:0002255	71.35	gold quality
colonic epithelium	UBERON:0000397	69.73	silver quality
left ovary	UBERON:0002119	69.69	gold quality
bone marrow cell	CL:0002092	69.42	silver quality
islet of Langerhans	UBERON:0000006	69.32	gold quality
left lobe of thyroid gland	UBERON:0001120	69.27	gold quality
body of pancreas	UBERON:0001150	69.26	gold quality
pancreas	UBERON:0001264	68.70	gold quality
thyroid gland	UBERON:0002046	67.90	gold quality
right lobe of thyroid gland	UBERON:0001119	66.74	gold quality
right ovary	UBERON:0002118	66.12	gold quality
adenohypophysis	UBERON:0002196	66.04	gold quality
adult mammalian kidney	UBERON:0000082	65.10	gold quality
lymph node	UBERON:0000029	64.72	gold quality
ovary	UBERON:0000992	64.66	gold quality
pituitary gland	UBERON:0000007	64.26	gold quality
adrenal tissue	UBERON:0018303	63.68	gold quality
ectocervix	UBERON:0012249	63.01	gold quality
body of uterus	UBERON:0009853	62.84	gold quality
minor salivary gland	UBERON:0001830	62.83	gold quality
cortical plate	UBERON:0005343	62.83	gold quality
metanephros cortex	UBERON:0010533	62.77	gold quality
endocervix	UBERON:0000458	62.75	gold quality
cortex of kidney	UBERON:0001225	62.32	gold quality
gall bladder	UBERON:0002110	61.86	gold quality
right adrenal gland	UBERON:0001233	61.25	gold quality
lower esophagus mucosa	UBERON:0035834	61.22	gold quality
ventricular zone	UBERON:0003053	61.07	gold quality
spleen	UBERON:0002106	61.04	gold quality
smooth muscle tissue	UBERON:0001135	60.76	gold quality
left uterine tube	UBERON:0001303	60.72	gold quality
ganglionic eminence	UBERON:0004023	60.72	gold quality
right adrenal gland cortex	UBERON:0035827	60.54	gold quality
saliva-secreting gland	UBERON:0001044	60.23	gold quality
left adrenal gland	UBERON:0001234	59.92	gold quality
mouth mucosa	UBERON:0003729	59.91	gold quality
left adrenal gland cortex	UBERON:0035825	59.79	gold quality
uterine cervix	UBERON:0000002	59.73	gold quality
omental fat pad	UBERON:0010414	59.60	gold quality
peritoneum	UBERON:0002358	59.55	gold quality
lower esophagus	UBERON:0013473	59.31	gold quality
body of stomach	UBERON:0001161	59.30	gold quality
lower esophagus muscularis layer	UBERON:0035833	59.29	gold quality
ascending aorta	UBERON:0001496	59.23	gold quality
thoracic aorta	UBERON:0001515	59.22	gold quality
adrenal gland	UBERON:0002369	59.17	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	58.89	gold quality
adrenal cortex	UBERON:0001235	58.57	gold quality
adipose tissue of abdominal region	UBERON:0007808	58.55	gold quality
kidney	UBERON:0002113	58.52	gold quality
hindlimb stylopod muscle	UBERON:0004252	58.52	gold quality
descending thoracic aorta	UBERON:0002345	58.46	gold quality
vagina	UBERON:0000996	58.43	gold quality
esophagus	UBERON:0001043	58.20	gold quality
upper lobe of left lung	UBERON:0008952	58.10	gold quality
vermiform appendix	UBERON:0001154	58.08	gold quality
leukocyte	CL:0000738	57.68	gold quality
prostate gland	UBERON:0002367	57.59	gold quality
stomach	UBERON:0000945	57.53	gold quality
esophagus mucosa	UBERON:0002469	57.38	gold quality
monocyte	CL:0000576	57.19	gold quality
muscle layer of sigmoid colon	UBERON:0035805	57.17	gold quality
blood	UBERON:0000178	56.82	gold quality
skin of leg	UBERON:0001511	56.80	gold quality
right atrium auricular region	UBERON:0006631	56.71	gold quality
female reproductive system	UBERON:0000474	56.66	gold quality
upper lobe of lung	UBERON:0008948	56.66	gold quality
skin of abdomen	UBERON:0001416	56.50	gold quality
mucosa of transverse colon	UBERON:0004991	56.50	gold quality
cardiac atrium	UBERON:0002081	56.28	gold quality
tonsil	UBERON:0002372	56.21	gold quality
metanephros	UBERON:0000081	56.13	gold quality
aorta	UBERON:0000947	55.82	gold quality
nasal cavity mucosa	UBERON:0001826	55.76	gold quality
left coronary artery	UBERON:0001626	55.35	gold quality
small intestine Peyer’s patch	UBERON:0003454	55.31	gold quality
right lung	UBERON:0002167	55.05	gold quality
calcaneal tendon	UBERON:0003701	54.86	gold quality
zone of skin	UBERON:0000014	54.73	gold quality
fundus of stomach	UBERON:0001160	54.71	gold quality
uterus	UBERON:0000995	54.60	gold quality
small intestine	UBERON:0002108	54.31	gold quality
mucosa of stomach	UBERON:0001199	54.23	gold quality
caecum	UBERON:0001153	54.14	gold quality
myometrium	UBERON:0001296	53.99	gold quality
coronary artery	UBERON:0001621	53.99	gold quality
granulocyte	CL:0000094	53.95	gold quality
anatomical system	UBERON:0000467	53.47	gold quality
apex of heart	UBERON:0002098	53.37	gold quality
popliteal artery	UBERON:0002250	53.24	gold quality
tibial artery	UBERON:0007610	53.24	gold quality
multicellular organism	UBERON:0000468	53.22	gold quality
material anatomical entity	UBERON:0000465	53.21	gold quality
lung	UBERON:0002048	52.99	gold quality
intestine	UBERON:0000160	52.68	gold quality
heart	UBERON:0000948	52.56	gold quality
colon	UBERON:0001155	52.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.07

Regulation

Is transcription factor: no

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
PIK3CD	protein-coding	5293
PIK3CD-AS1	ncRNA	644997
CTNNBIP1-AS1	ncRNA	139355239
CLSTN1	protein-coding	22883
CTNNBIP1	protein-coding	56998
TMEM201	protein-coding	199953
SLC25A33	protein-coding	84275

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 5 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

chr1p36, MANNO_MIDBRAIN_NEUROTYPES_HPERIC, HAY_BONE_MARROW_PLASMA_CELL, HOEK_T_CELL_2011_2012_TIV_ADULT_3DY_UP, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL

ncRNA interactions

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

5 interaction partners:

Partner	Partner type	Level	Source
RNU1-148P	snRNA	RNA-RNA	RISE database
AJAP1	mRNA	RNA-RNA	RISE database
IGF2BP3	protein	RNA-Protein	High-throughput data
SOX2	protein	RNA-Protein	High-throughput data
IGF2BP1	protein	RNA-Protein	High-throughput data

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No curated drug or pharmacology associations for this gene.