Fxr1 FMR1 autosomal homolog 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Fxr1provided by MGI
Official Full Name: FMR1 autosomal homolog 1provided by MGI
Primary source: MGI:MGI:104860
See related: Ensembl:ENSMUSG00000027680 AllianceGenome:MGI:104860
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Fxr1h; Fxr1p; 1110050J02Rik; 9530073J07Rik
Summary: Enables G-quadruplex RNA binding activity and mRNA 3'-UTR binding activity. Involved in skeletal muscle organ development. Acts upstream of or within muscle organ development and negative regulation of translation. Located in several cellular components, including costamere; dendritic spine; and glutamatergic synapse. Part of polysome. Is expressed in several structures, including central nervous system; gut; musculature; sensory organ; and urinary system. Orthologous to human FXR1 (FMR1 autosomal homolog 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in testis adult (RPKM 55.6), CNS E11.5 (RPKM 32.4) and 20 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 A3; 3 16.41 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (34074133..34124129)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (34020058..34069980)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

FXR1 impedes the development of osteoarthritis by targeting SND1.
Title: FXR1 impedes the development of osteoarthritis by targeting SND1.
ARL6IP1 mediates small-molecule-induced alleviation of Alzheimer pathology through FXR1-dependent BACE1 translation initiation.
Title: ARL6IP1 mediates small-molecule-induced alleviation of Alzheimer pathology through FXR1-dependent BACE1 translation initiation.
Genetic Deletion of FXR1 Reduces Intimal Hyperplasia and Induces Senescence in Vascular Smooth Muscle Cells.
Title: Genetic Deletion of FXR1 Reduces Intimal Hyperplasia and Induces Senescence in Vascular Smooth Muscle Cells.
LLPS of FXR1 drives spermiogenesis by activating translation of stored mRNAs.
Title: LLPS of FXR1 drives spermiogenesis by activating translation of stored mRNAs.
Skeletal muscle proteome expression differentiates severity of cancer cachexia in mice and identifies loss of fragile X mental retardation syndrome-related protein 1.
Title: Skeletal muscle proteome expression differentiates severity of cancer cachexia in mice and identifies loss of fragile X mental retardation syndrome-related protein 1.
LncRNA TUG1 regulates ApoM to promote atherosclerosis progression through miR-92a/FXR1 axis.
Title: LncRNA TUG1 regulates ApoM to promote atherosclerosis progression through miR-92a/FXR1 axis.
Fxr1 regulates sleep and synaptic homeostasis.
Title: Fxr1 regulates sleep and synaptic homeostasis.
FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells.
Title: FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells.
Here, we will review the unexpected roles of FXRalpha on the male reproductive tract. FXRa has been demonstrated to play functions in the regulation of testicular and prostate homeostasis. Even though additional studies are needed to confirm these findings in humans, the reviewed reports open new field of research to better define the effects of bile acid-FXRa signaling pathways on fertility disorders and cancers
Title: Farnesoid X receptor alpha (FXRα) is a critical actor of the development and pathologies of the male reproductive system.
FXR deficiency increased hepatic steatosis and altered bile acid pool composition, contributing to worsened liver toxicity.
Title: FXR deficiency alters bile acid pool composition and exacerbates chronic alcohol induced liver injury.

Submit: New GeneRIF Correction See all GeneRIFs (25)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Endonuclease-mediated (9) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BI274570 (e-PCR)
- UniSTS:249125

BI281166 (e-PCR)
- UniSTS:249408

Fxr1h (e-PCR), detects polymorphism
- UniSTS:498301

UniSTS:479111 (e-PCR)
- UniSTS:479111

Fxr1h (e-PCR), detects polymorphism
- UniSTS:479111

AI851072 (e-PCR)
- UniSTS:178825

AA959924 (e-PCR)
- UniSTS:185527

X90875 (e-PCR)
- UniSTS:125882

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA strand annealing activity	ISO Inferred from Sequence Orthology more info
enables mRNA 3'-UTR AU-rich region binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA 3'-UTR AU-rich region binding	ISO Inferred from Sequence Orthology more info
enables mRNA 3'-UTR binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA 3'-UTR binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables molecular condensate scaffold activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables ribonucleoprotein complex binding	IDA Inferred from Direct Assay more info	PubMed
enables translation regulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in animal organ development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in dentate gyrus development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA destabilization	ISO Inferred from Sequence Orthology more info
involved_in mRNA transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in muscle organ development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle organ development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of long-term synaptic potentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of tumor necrosis factor production	IDA Inferred from Direct Assay more info	PubMed
involved_in non-membrane-bounded organelle assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear pore complex assembly	ISO Inferred from Sequence Orthology more info
involved_in nuclear pore localization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of long-term neuronal synaptic plasticity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of miRNA-mediated gene silencing	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of translation	ISO Inferred from Sequence Orthology more info
involved_in post-transcriptional regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in post-transcriptional regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of circadian sleep/wake cycle, sleep	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA stability	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of neurogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synaptic transmission, glutamatergic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of translation	IEA Inferred from Electronic Annotation more info
involved_in regulation of translation at presynapse, modulating synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal muscle organ development	IDA Inferred from Direct Assay more info	PubMed
involved_in skeletal muscle organ development	ISO Inferred from Sequence Orthology more info
involved_in spermatid development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in costamere	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasmic ribonucleoprotein granule	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasmic stress granule	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasmic stress granule	ISO Inferred from Sequence Orthology more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in dendritic spine	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in intracellular non-membrane-bounded organelle	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nuclear envelope	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynapse	IDA Inferred from Direct Assay more info	PubMed
located_in ribonucleoprotein granule	IDA Inferred from Direct Assay more info	PubMed
located_in ribosome	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: RNA-binding protein FXR1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001113188.3 → NP_001106659.1 RNA-binding protein FXR1 isoform 1

See identical proteins and their annotated locations for NP_001106659.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as isoform e).

Source sequence(s)

AC068294, AC115078

Consensus CDS

CCDS50891.1

UniProtKB/Swiss-Prot

Q61584, Q8VCU4, Q9R1E2, Q9R1E3, Q9R1E4, Q9R1E5, Q9WUA7, Q9WUA8, Q9WUA9

Related

ENSMUSP00000001620.9, ENSMUST00000001620.13

Conserved Domains (6) summary

smart00322
Location:221 → 280

KH; K homology RNA-binding domain

cd00105
Location:286 → 352

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam05641
Location:62 → 118

Agenet; Agenet domain

pfam12235
Location:354 → 465

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:491 → 563

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:610 → 676

FXR_C3; Fragile X-related 1 protein C-terminal region 3
NM_001113189.3 → NP_001106660.1 RNA-binding protein FXR1 isoform 2

See identical proteins and their annotated locations for NP_001106660.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks alternate in-frame segments in both the mid-coding and 3' coding regions, compared to variant 1, resulting in a shorter protein (isoform 2, also known as isoform d), compared to isoform 1.

Source sequence(s)

AC068294, AC115078

Consensus CDS

CCDS79896.1

UniProtKB/Swiss-Prot

Q61584

Related

ENSMUSP00000142441.2, ENSMUST00000197694.5

Conserved Domains (6) summary

smart00322
Location:221 → 280

KH; K homology RNA-binding domain

cd00105
Location:286 → 352

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam05641
Location:62 → 118

Agenet; Agenet domain

pfam12235
Location:354 → 436

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:462 → 535

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:554 → 620

FXR_C3; Fragile X-related 1 protein C-terminal region 3
NM_001428474.1 → NP_001415403.1 RNA-binding protein FXR1 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate exon in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 4, also known as isoform c), compared to isoform 1.

Source sequence(s)

AC068294, AC115078
NM_001428475.1 → NP_001415404.1 RNA-binding protein FXR1 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame segment in the 3' coding regions, compared to variant 1, resulting in a shorter protein (isoform 5, also known as isoform f), compared to isoform 1.

Source sequence(s)

AC068294, AC115078
NM_001428476.1 → NP_001415405.1 RNA-binding protein FXR1 isoform 6

Status: VALIDATED

Description

Transcript Variant: This variant (6) lacks two alternate exons in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 6, also known as isoform b), compared to isoform 1.

Source sequence(s)

AC068294, AC115078

UniProtKB/TrEMBL

A0A0G2JEP0
NM_008053.4 → NP_032079.1 RNA-binding protein FXR1 isoform 3

See identical proteins and their annotated locations for NP_032079.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 3' UTR, and lacks an alternate in-frame segment in the mid-coding region and two alternate exons in the 3' coding region, compared to variant 1. The resulting protein (isoform 3, also known as isoform a) contains a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AC068294, AC115078

Consensus CDS

CCDS50890.1

UniProtKB/TrEMBL

A0A0H2UH27

Related

ENSMUSP00000143392.2, ENSMUST00000200392.5

Conserved Domains (5) summary

smart00322
Location:221 → 280

KH; K homology RNA-binding domain

cd00105
Location:286 → 352

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam05641
Location:62 → 118

Agenet; Agenet domain

pfam12235
Location:354 → 436

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:462 → 535

FXR_C1; Fragile X-related 1 protein C-terminal region 2

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

34074133..34124129

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006535400.2 → XP_006535463.1 RNA-binding protein FXR1 isoform X1

UniProtKB/Swiss-Prot

Q61584

Conserved Domains (8) summary

smart00322
Location:221 → 280

KH; K homology RNA-binding domain

cd00105
Location:286 → 352

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam05641
Location:62 → 117

Agenet; Agenet domain

pfam12235
Location:354 → 465

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:491 → 564

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:583 → 649

FXR_C3; Fragile X-related 1 protein C-terminal region 3

pfam17904
Location:123 → 207

KH_9; FMRP KH0 domain

pfam18336
Location:4 → 52

Tudor_FRX1; Fragile X mental retardation Tudor domain
XM_006535402.2 → XP_006535465.1 RNA-binding protein FXR1 isoform X4

Related

ENSMUSP00000142847.2, ENSMUST00000198051.5

Conserved Domains (7) summary

smart00322
Location:221 → 280

KH; K homology RNA-binding domain

cd00105
Location:286 → 352

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam05641
Location:62 → 117

Agenet; Agenet domain

pfam12235
Location:354 → 465

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:491 → 564

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam17904
Location:123 → 207

KH_9; FMRP KH0 domain

pfam18336
Location:4 → 52

Tudor_FRX1; Fragile X mental retardation Tudor domain
XM_006535401.2 → XP_006535464.1 RNA-binding protein FXR1 isoform X2

UniProtKB/Swiss-Prot

Q61584

Conserved Domains (8) summary

smart00322
Location:221 → 280

KH; K homology RNA-binding domain

cd00105
Location:286 → 352

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam05641
Location:62 → 117

Agenet; Agenet domain

pfam12235
Location:354 → 436

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:462 → 534

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:581 → 647

FXR_C3; Fragile X-related 1 protein C-terminal region 3

pfam17904
Location:123 → 207

KH_9; FMRP KH0 domain

pfam18336
Location:4 → 52

Tudor_FRX1; Fragile X mental retardation Tudor domain
XM_036162897.1 → XP_036018790.1 RNA-binding protein FXR1 isoform X6

UniProtKB/TrEMBL

A0A0H2UH27

Conserved Domains (6) summary

pfam12235
Location:269 → 380

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:406 → 479

FXR_C1; Fragile X-related 1 protein C-terminal region 2

cd22504
Location:38 → 114

KH_I_FXR1_rpt1; first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22507
Location:133 → 195

KH_I_FXR1_rpt2; second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22510
Location:196 → 273

KH_I_FXR1_rpt3; third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cl02573
Location:1 → 41

Tudor_SF; Tudor domain superfamily
XM_036162895.1 → XP_036018788.1 RNA-binding protein FXR1 isoform X3

Conserved Domains (7) summary

pfam12235
Location:269 → 380

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:406 → 479

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:525 → 591

FXR_C3; Fragile X-related 1 protein C-terminal region 3

cd22504
Location:38 → 114

KH_I_FXR1_rpt1; first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22507
Location:133 → 195

KH_I_FXR1_rpt2; second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22510
Location:196 → 273

KH_I_FXR1_rpt3; third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cl02573
Location:1 → 41

Tudor_SF; Tudor domain superfamily
XM_036162896.1 → XP_036018789.1 RNA-binding protein FXR1 isoform X5

Conserved Domains (7) summary

pfam12235
Location:269 → 380

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:406 → 479

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:498 → 564

FXR_C3; Fragile X-related 1 protein C-terminal region 3

cd22504
Location:38 → 114

KH_I_FXR1_rpt1; first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22507
Location:133 → 195

KH_I_FXR1_rpt2; second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22510
Location:196 → 273

KH_I_FXR1_rpt3; third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cl02573
Location:1 → 41

Tudor_SF; Tudor domain superfamily