HOXB-AS3

Summary

HOXB-AS3 (HOXB cluster antisense RNA 3, HGNC:40283) is a long non-coding RNA gene on chromosome 17q21.32. Blocks the binding of HNRNPA1 to the intronic sequences flanking exon 9 of the PKM gene by competitively binding to the HNRNPA1 RGG-box motif.

Involved in negative regulation of pre-miRNA processing; protein stabilization; and regulation of RNA splicing.

Source: NCBI Gene 404266 — RefSeq curated summary.

At a glance

• Gene type: non-coding (lncRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40283
Approved symbol	HOXB-AS3
Name	HOXB cluster antisense RNA 3
Location	17q21.32
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000233101
Ensembl biotype	lncRNA
Entrez	404266
RNAcentral	URS000075E8D0 — lncRNA, 611 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 24 lncRNA

ENST00000429755, ENST00000460041, ENST00000465846, ENST00000466037, ENST00000467155, ENST00000474040, ENST00000474324, ENST00000476204, ENST00000477144, ENST00000480872, ENST00000481995, ENST00000487849, ENST00000491264, ENST00000492897, ENST00000494420, ENST00000717436, ENST00000717437, ENST00000717438, ENST00000717439, ENST00000717472, ENST00000717473, ENST00000717474, ENST00000717475, ENST00000717476

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000429755 — 3 exons

Exon	Start	End
ENSE00002385545	48592211	48592364
ENSE00003555919	48600447	48600545
ENSE00004032507	48602075	48602343

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 96.03.

FANTOM5 (CAGE): breadth broad, TPM avg 3.0702 / max 587.5726, expressed in 367 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161446	2.4849	247
161448	0.2814	134
161440	0.1150	64
161447	0.0507	21
161439	0.0454	20
161450	0.0377	16
161449	0.0368	16
161438	0.0182	6

Top tissues by expression

237 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	96.03	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.67	gold quality
metanephros cortex	UBERON:0010533	93.82	gold quality
rectum	UBERON:0001052	91.08	gold quality
transverse colon	UBERON:0001157	90.64	gold quality
adult mammalian kidney	UBERON:0000082	89.57	gold quality
mucosa of stomach	UBERON:0001199	89.13	gold quality
colon	UBERON:0001155	87.37	gold quality
large intestine	UBERON:0000059	86.71	gold quality
pancreatic ductal cell	CL:0002079	86.59	silver quality
right uterine tube	UBERON:0001302	86.57	gold quality
metanephros	UBERON:0000081	86.26	gold quality
kidney	UBERON:0002113	85.26	gold quality
intestine	UBERON:0000160	85.18	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.16	gold quality
cauda epididymis	UBERON:0004360	83.66	gold quality
seminal vesicle	UBERON:0000998	82.38	gold quality
right lung	UBERON:0002167	82.29	gold quality
cortex of kidney	UBERON:0001225	82.16	gold quality
colonic epithelium	UBERON:0000397	81.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.45	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.16	gold quality
small intestine	UBERON:0002108	81.12	gold quality
spinal cord	UBERON:0002240	79.47	gold quality
mucosa of transverse colon	UBERON:0004991	78.87	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	78.48	gold quality
smooth muscle tissue	UBERON:0001135	78.41	gold quality
upper lobe of left lung	UBERON:0008952	78.10	gold quality
omental fat pad	UBERON:0010414	78.10	gold quality
peritoneum	UBERON:0002358	78.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.21

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 9)

• A peptide encoded by a putative lncRNA HOXB-AS3 suppresses colon cancer growth. (PMID:28985503)
• Highly expressed HOXB-AS3 was confirmed to promote the proliferation of hepatocellular carcinoma cells and inhibit apoptosis, and the mechanism was related to the regulatory role of HOXB-AS3 in p53 expression by binding to DNMT1 promoter. (PMID:30402841)
• This study uncovers a promoting role of HOXB-AS3 in myeloid malignancies and identifies the prognostic value of HOXB-AS3 expression in acute myeloid leukemia and myelodysplastic syndromepatients, particularly in the lower-risk group. (PMID:31234830)
• Data suggest that in the context of nucleophosmin 1 (NPM1) mutations, the long non-coding RNA HOXB-AS3 (HOXB-AS3) overexpression acts as a compensatory mechanism, which allows adequate protein production in leukemic blasts. (PMID:31767858)
• lncRNA HOXB-AS3 exacerbates proliferation, migration, and invasion of lung cancer via activating the PI3K-AKT pathway. (PMID:32039488)
• LncRNA HOXB-AS3 promotes growth, invasion and migration of epithelial ovarian cancer by altering glycolysis. (PMID:33148416)
• Long non-coding RNA (lncRNA) HOXB-AS3 promotes cell proliferation and inhibits apoptosis by regulating ADAM9 expression through targeting miR-498-5p in endometrial carcinoma. (PMID:34187214)
• Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage. (PMID:34280202)
• Alternative splicing of HOXB-AS3 underlie the promoting effect of nuclear m6A reader YTHDC1 on the self-renewal of leukemic stem cells in acute myeloid leukemia. (PMID:36906205)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

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

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.