Firre MGI Mouse Gene Detail - MGI:2147989 - functional intergenic repeating RNA element

Symbol

Firre
Name

functional intergenic repeating RNA element
Synonyms

5830467J12Rik, 6720401G13Rik

Feature Type

lncRNA gene
IDs

MGI:2147989
NCBI Gene: 103012
Alliance

gene page
Transcription Start Sites

3 TSS

Sequence Map

ChrX:49651997-49724198 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome X, 26.53 cM
Mapping Data

2 experiments

SNPs within 2kb

2812 from dbSNP Build 142
Strain Annotations

16

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2147989	lncRNA gene	ChrX:49644621-49724198 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0015777	unclassified non-coding RNA gene	ChrX:45696757-45781912 (-)
A/J	MGP_AJ_G0015754	unclassified non-coding RNA gene	ChrX:45565558-45651331 (-)
AKR/J	MGP_AKRJ_G0015716	unclassified non-coding RNA gene	ChrX:46798339-46907763 (-)
BALB/cJ	MGP_BALBcJ_G0015715	unclassified non-coding RNA gene	ChrX:45158707-45253196 (-)
C3H/HeJ	MGP_C3HHeJ_G0015535	unclassified non-coding RNA gene	ChrX:45986953-46062219 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0016169	unclassified non-coding RNA gene	ChrX:46750012-46884950 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0013893	unclassified non-coding RNA gene	ChrX:43176997-43246304 (-)
CAST/EiJ	MGP_CASTEiJ_G0015090	unclassified non-coding RNA gene	ChrX:33407547-33506091 (-)
CBA/J	MGP_CBAJ_G0015515	unclassified non-coding RNA gene	ChrX:48097713-48181076 (-)
DBA/2J	MGP_DBA2J_G0015613	unclassified non-coding RNA gene	ChrX:45416304-45503413 (-)
FVB/NJ	no annotation
LP/J	MGP_LPJ_G0015695	unclassified non-coding RNA gene	ChrX:46029865-46116289 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0015641	unclassified non-coding RNA gene	ChrX:49597251-49712394 (-)
NZO/HlLtJ	no annotation
PWK/PhJ	MGP_PWKPhJ_G0014872	unclassified non-coding RNA gene	ChrX:32889199-33034688 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0014659	unclassified non-coding RNA gene	ChrX:34207416-34309204 (-)
WSB/EiJ	MGP_WSBEiJ_G0015194	unclassified non-coding RNA gene	ChrX:45151966-45234739 (-)

Human Ortholog

FIRRE, firre intergenic repeating RNA element

Vertebrate Orthologs

1

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FIRRE, firre intergenic repeating RNA element
Synonyms

LINC01200
Links

HGNC:49627

NCBI Gene ID: 286467
Chr Location

Xq26.2; chrX:131688779-131830862 (-) GRCh38

MGI Vertebrate Homology

Firre stringent orthology
1 human;1 mouse
HCOP

vertebrate homology predictions: FIRRE
Gene Tree

Firre

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Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
1 phenotype from multigenic genotypes
9 phenotype references

All Mutations and Alleles

16
Endonuclease-mediated

1
Gene trapped

13
Targeted

2
Find Mice (IMSR)

14 strains or lines available

Mice homozygous for a null allele are viable and fertile with no defect in random or imprinted XCI.

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All GO Annotations

3
GO References

1

Molecular Function

No experimental evidence to support Molecular Function annotation, following literature review. See J:73796.

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1158
Tissues

87
cDNA Data

92
Literature Summary

4

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

56
RefSeq

1
UniProt

1

Ensembl

ENSMUSG00000085396 (Evidence)
NCBI Gene

103012

			Length	Strain/Species	Flank
genomic	103012	NCBI Gene Model \| MGI Sequence Detail	72202	C57BL/6J	± kb
transcript	NR_015505	RefSeq \| MGI Sequence Detail	5832	C57BL/6
polypeptide	Q3V1H2	UniProt \| EBI \| MGI Sequence Detail	85	Not Applicable

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UniProt

1 Sequence

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All nucleic 92

cDNA 92

Microarray probesets 4

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MGI:2442400

Summaries

All 32

Developmental Gene Expression 4

Gene Ontology 1

Phenotypes 9
Earliest

J:93290 Araki K, et al., Exchangeable gene trap using the Cre/mutated lox system. Cell Mol Biol (Noisy-Le-Grand). 1999 Jul;45(5):737-50
Latest

J:299861 Fang H, et al., Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nat Commun. 2020 Nov 27;11(1):6053

TSS for Firre:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr163315	ChrX:49724160-49724205 (-)	15 bp
Tssr163314	ChrX:49724124-49724149 (-)	61 bp
Tssr163313	ChrX:49674364-49674368 (-)	49,832 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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