FIRRE

Summary

FIRRE (firre intergenic repeating RNA element, HGNC:49627) is a long non-coding RNA gene on chromosome Xq26.2.

This gene produces a long RNA containing a repeating sequence. This RNA interacts with heterogeneous nuclear ribonucleoprotein U and coats chromosomes, where it plays an important role in the maintenance of repressive chromatin. This transcript can also act post-transcriptionally to regulate the stability of mRNAs during the innate immune response.

Source: NCBI Gene 286467 — 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:49627
Approved symbol	FIRRE
Name	firre intergenic repeating RNA element
Location	Xq26.2
Locus type	RNA, long non-coding
Status	Approved
Aliases	LINC01200
Ensembl gene	ENSG00000213468
Ensembl biotype	lncRNA
OMIM	300999
Entrez	286467
RNAcentral	URS00002F3F76 — lncRNA, 2928 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 33 lncRNA, 1 retained_intron

ENST00000427391, ENST00000637577, ENST00000647966, ENST00000648028, ENST00000649391, ENST00000649541, ENST00000650184, ENST00000653136, ENST00000654978, ENST00000656586, ENST00000657242, ENST00000658060, ENST00000658376, ENST00000662867, ENST00000663405, ENST00000665076, ENST00000668308, ENST00000842154, ENST00000842155, ENST00000842156, ENST00000842157, ENST00000842158, ENST00000842159, ENST00000842160, ENST00000842161, ENST00000842162, ENST00000842163, ENST00000842164, ENST00000842165, ENST00000842166, ENST00000842167, ENST00000842168, ENST00000842169, ENST00000842170

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000427391 — 13 exons

Exon	Start	End
ENSE00001594498	131711651	131711720
ENSE00001658652	131702652	131703518
ENSE00001659046	131825222	131825365
ENSE00001674554	131749306	131749458
ENSE00001731274	131768549	131768696
ENSE00001734033	131709498	131709556
ENSE00001738500	131783887	131784039
ENSE00001750021	131794324	131794466
ENSE00001752569	131755598	131755746
ENSE00001772311	131804972	131805037
ENSE00001775093	131830292	131830643
ENSE00001789362	131795809	131796331
ENSE00001797184	131756611	131756709

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 84.85.

FANTOM5 (CAGE): breadth broad, TPM avg 6.3020 / max 289.5386, expressed in 837 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200489	5.4210	752
200488	0.4846	196
200490	0.2944	164
200487	0.1020	52

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	84.85	gold quality
sural nerve	UBERON:0015488	76.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.30	gold quality
body of pancreas	UBERON:0001150	75.13	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.49	gold quality
bone marrow cell	CL:0002092	72.96	gold quality
pancreas	UBERON:0001264	67.63	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	66.82	gold quality
secondary oocyte	CL:0000655	66.80	gold quality
ventricular zone	UBERON:0003053	65.42	gold quality
monocyte	CL:0000576	65.22	gold quality
leukocyte	CL:0000738	64.83	gold quality
spinal cord	UBERON:0002240	64.38	gold quality
tibial nerve	UBERON:0001323	62.39	gold quality
granulocyte	CL:0000094	61.76	gold quality
calcaneal tendon	UBERON:0003701	61.27	gold quality
spleen	UBERON:0002106	60.89	gold quality
hindlimb stylopod muscle	UBERON:0004252	59.74	gold quality
adrenal tissue	UBERON:0018303	59.01	gold quality
lymph node	UBERON:0000029	58.91	gold quality
ganglionic eminence	UBERON:0004023	58.87	gold quality
epithelium of nasopharynx	UBERON:0001951	58.46	gold quality
corpus callosum	UBERON:0002336	58.20	gold quality
substantia nigra	UBERON:0002038	57.90	gold quality
vermiform appendix	UBERON:0001154	56.32	gold quality
amygdala	UBERON:0001876	56.25	gold quality
tonsil	UBERON:0002372	56.09	gold quality
bone marrow	UBERON:0002371	56.06	gold quality
smooth muscle tissue	UBERON:0001135	55.99	gold quality
endocervix	UBERON:0000458	55.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.98

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 10)

• this study shows a new regulatory role for NF-kappaB-responsive FIRRE in the posttranscriptional regulation of inflammatory genes in the innate immune system (PMID:28993514)
• neither the deletion of the CTCF locus nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter topologically associated domains in a sex-specific or allele-specific manner (PMID:29654311)
• RMST and FIRRE, genes with established roles in neurogenesis and topological organisation of chromosomal domains respectively, are processed as circular lncRNAs with only minor linear species (PMID:29678151)
• FIRRE is transcriptionally activated by MYC. (PMID:30739786)
• LncRNA FIRRE functions as a tumor promoter by interaction with PTBP1 to stabilize BECN1 mRNA and facilitate autophagy. (PMID:35110535)
• LncRNA FIRRE stimulates PTBP1-induced Smurf2 decay, stabilizes B-cell receptor, and promotes the development of diffuse large B-cell lymphoma. (PMID:35416325)
• LncRNA FIRRE promotes the proliferation and metastasis of hepatocellular carcinoma by regulating the expression of PXN through interacting with MBNL3. (PMID:35988459)
• Microarray analysis identifies lncFirre as a potential regulator of obesity-related acute lung injury. (PMID:38307237)
• Increased expression of long non-coding RNA FIRRE promotes hepatocellular carcinoma by HuR-CyclinD1 axis signaling. (PMID:38556083)
• The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation. (PMID:39122712)

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.