HAO2-IT1
gene geneOn this page
Summary
HAO2-IT1 (HAO2 intronic transcript 1, HGNC:41342) is a long non-coding RNA gene on chromosome 1p12.
At a glance
- Gene type: non-coding (lncRNA) — no protein product.
- GTEx eGene: eQTL in 2 tissues, sQTL in 0 (q < 0.05)
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:41342 |
| Approved symbol | HAO2-IT1 |
| Name | HAO2 intronic transcript 1 |
| Location | 1p12 |
| Locus type | RNA, long non-coding |
| Status | Approved |
| Ensembl gene | ENSG00000230921 |
| Ensembl biotype | lncRNA |
| Entrez | 100874270 |
| RNAcentral | URS00005B433E — ncRNA, 311 nt, 2 organism(s) |
Gene structure
Transcript identifiers
Ensembl transcripts: 1 — 1 lncRNA
Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 5: 1
ENST00000419144
RefSeq mRNA: 0
Canonical transcript exons
ENST00000419144 — 2 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001614027 | 119368946 | 119369008 |
| ENSE00001763846 | 119370084 | 119370331 |
Expression profiles
Bgee: expression breadth broad, 68 present calls, max score 73.89.
Highest expression (Bgee): liver, lobe of liver, adrenal gland cortex, adrenal gland, monocyte.
Genetic regulation across tissues (GTEx eQTL / sQTL)
HAO2-IT1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 2 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.
2 significant tissue × QTL associations:
| Tissue | QTL | q-value | Slope | Lead variant |
|---|---|---|---|---|
| Liver | eqtl | 3.3e-11 | +0.59 | 1:119370216:T:G |
| Kidney Cortex | eqtl | 8.9e-03 | +0.70 | 1:119370216:T:G |
Top tissues by expression
68 tissues by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| liver | UBERON:0002107 | 73.89 | gold quality |
| right lobe of liver | UBERON:0001114 | 71.14 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 66.15 | gold quality |
| right adrenal gland | UBERON:0001233 | 65.85 | gold quality |
| adrenal gland | UBERON:0002369 | 64.61 | gold quality |
| monocyte | CL:0000576 | 64.29 | gold quality |
| left adrenal gland | UBERON:0001234 | 64.21 | gold quality |
| prefrontal cortex | UBERON:0000451 | 62.81 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 62.68 | gold quality |
| blood | UBERON:0000178 | 61.61 | gold quality |
| pancreas | UBERON:0001264 | 60.83 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 60.51 | gold quality |
| body of pancreas | UBERON:0001150 | 60.50 | gold quality |
| corpus callosum | UBERON:0002336 | 60.41 | gold quality |
| kidney | UBERON:0002113 | 58.34 | gold quality |
| adult mammalian kidney | UBERON:0000082 | 57.88 | gold quality |
| small intestine | UBERON:0002108 | 57.54 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 57.49 | gold quality |
| cortex of kidney | UBERON:0001225 | 56.09 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 55.33 | gold quality |
| intestine | UBERON:0000160 | 54.49 | gold quality |
| adenohypophysis | UBERON:0002196 | 54.16 | gold quality |
| multicellular organism | UBERON:0000468 | 53.76 | gold quality |
| tibial artery | UBERON:0007610 | 53.09 | gold quality |
| right ovary | UBERON:0002118 | 51.81 | gold quality |
| Ammon’s horn | UBERON:0001954 | 51.63 | gold quality |
| frontal cortex | UBERON:0001870 | 51.42 | gold quality |
| thoracic aorta | UBERON:0001515 | 51.27 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 51.27 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 50.77 | gold quality |
| lung | UBERON:0002048 | 50.44 | gold quality |
| spleen | UBERON:0002106 | 50.41 | gold quality |
| substantia nigra | UBERON:0002038 | 50.02 | gold quality |
| esophagus mucosa | UBERON:0002469 | 49.97 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 49.88 | gold quality |
| stomach | UBERON:0000945 | 49.77 | gold quality |
| subcutaneous adipose tissue | UBERON:0002190 | 49.70 | gold quality |
| right frontal lobe | UBERON:0002810 | 49.68 | gold quality |
| brain | UBERON:0000955 | 49.41 | gold quality |
| ascending aorta | UBERON:0001496 | 49.36 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 49.14 | gold quality |
| rectum | UBERON:0001052 | 49.10 | gold quality |
| body of stomach | UBERON:0001161 | 49.08 | gold quality |
| heart | UBERON:0000948 | 48.67 | gold quality |
| putamen | UBERON:0001874 | 48.29 | gold quality |
| prostate gland | UBERON:0002367 | 48.25 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 48.13 | gold quality |
| amygdala | UBERON:0001876 | 47.98 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 47.98 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 47.41 | gold quality |
| skin of abdomen | UBERON:0001416 | 47.07 | gold quality |
| hypothalamus | UBERON:0001898 | 47.05 | gold quality |
| omental fat pad | UBERON:0010414 | 47.01 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 46.88 | gold quality |
| left ovary | UBERON:0002119 | 46.81 | gold quality |
| nucleus accumbens | UBERON:0001882 | 45.90 | gold quality |
| transverse colon | UBERON:0001157 | 45.72 | gold quality |
| skin of leg | UBERON:0001511 | 45.35 | gold quality |
| caudate nucleus | UBERON:0001873 | 44.96 | gold quality |
| right lung | UBERON:0002167 | 44.78 | gold quality |
| thoracic mammary gland | UBERON:0005200 | 43.70 | gold quality |
| pituitary gland | UBERON:0000007 | 43.58 | gold quality |
| tibial nerve | UBERON:0001323 | 42.85 | silver quality |
| right atrium auricular region | UBERON:0006631 | 42.30 | silver quality |
| vagina | UBERON:0000996 | 42.26 | silver quality |
| left lobe of thyroid gland | UBERON:0001120 | 42.11 | silver quality |
| metanephros cortex | UBERON:0010533 | 39.77 | silver quality |
| left testis | UBERON:0004533 | 26.61 | silver quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 1.63 |
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 |
|---|---|---|
| WARS2 | protein-coding | 10352 |
| LINC01780 | ncRNA | 105378934 |
| HAO2 | protein-coding | 51179 |
| WARS2-AS1 | ncRNA | 101929147 |
| HSD3B2 | protein-coding | 3284 |
Protein
Non-coding RNA — no protein product.
Function
Gene-set membership (MSigDB)
This non-coding RNA is a member of 3 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).
chr1p12, MAFG_TARGET_GENES, CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN
ncRNA interactions
Experimentally supported non-coding-RNA interaction partners (NPInter).
2 interaction partners:
| Partner | Partner type | Level | Source |
|---|---|---|---|
| FBL | protein | RNA-Protein | GSE77027 |
| KHDRBS2 | protein | RNA-Protein | High-throughput data |
Disease & clinical
No curated disease, variant, or cancer-driver associations.
Drugs & pharmacology
ncRNA–drug associations
Curated non-coding-RNA → drug associations (drug response / resistance / target).
1 ncRNA–drug associations:
| Drug | Relation | Effect | Condition |
|---|---|---|---|
| Gemcitabine | drug_resistance | sensitive | cell line (SNU-245) |
Related Atlas pages
- Associated drugs (ncRNA: response / resistance): Gemcitabine