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

Gene ID: 14359, updated on 2-Nov-2024

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 mRNA 3'-UTR AU-rich region binding activity; molecular condensate scaffold activity; and ribonucleoprotein complex binding activity. Involved in several processes, including dentate gyrus development; modulation of chemical synaptic transmission; and regulation of gene expression. Located in several cellular components, including costamere; dendritic spine; and ribosome. Is active in several cellular components, including glutamatergic synapse; intracellular non-membrane-bounded organelle; and postsynapse. Is expressed in several structures, including central nervous system; gut; heart; musculature; and sensory organ. Human ortholog(s) of this gene implicated in congenital myopathy 9A and congenital myopathy 9B. Orthologous to human FXR1 (FMR1 autosomal homolog 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis adult (RPKM 55.6), CNS E11.5 (RPKM 32.4) and 20 other tissues See more
Orthologs
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Genomic context

See Fxr1 in Genome Data Viewer
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_000069.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_07364 Neighboring gene predicted gene, 46833 Neighboring gene STARR-seq mESC enhancer starr_07366 Neighboring gene calcium regulated heat stable protein 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_07367 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 Neighboring gene STARR-seq mESC enhancer starr_07368 Neighboring gene SET translocation pseudogene Neighboring gene predicted gene, 52623

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 RNA strand annealing activity ISS
Inferred from Sequence or Structural Similarity
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 AU-rich region binding ISS
Inferred from Sequence or Structural Similarity
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 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein heterodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
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
 
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 destabilization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in mRNA transport IBA
Inferred from Biological aspect of Ancestor
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 muscle organ development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of inflammatory response ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of inflammatory response ISS
Inferred from Sequence or Structural Similarity
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 IEA
Inferred from Electronic Annotation
more info
 
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 complex assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in nuclear pore localization ISO
Inferred from Sequence Orthology
more info
 
involved_in nuclear pore localization ISS
Inferred from Sequence or Structural Similarity
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 miRNA-mediated gene silencing ISS
Inferred from Sequence or Structural Similarity
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 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 
Component Evidence Code Pubs
located_in axon IDA
Inferred from Direct Assay
more info
PubMed 
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
 
located_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 ribonucleoprotein granule ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in cytoplasmic stress granule IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasmic stress granule IEA
Inferred from Electronic Annotation
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 nuclear envelope ISS
Inferred from Sequence or Structural Similarity
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 

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)

  1. NM_001113188.3NP_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:221280
    KH; K homology RNA-binding domain
    cd00105
    Location:286352
    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:62118
    Agenet; Agenet domain
    pfam12235
    Location:354465
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:491563
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:610676
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
  2. NM_001113189.3NP_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:221280
    KH; K homology RNA-binding domain
    cd00105
    Location:286352
    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:62118
    Agenet; Agenet domain
    pfam12235
    Location:354436
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:462535
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:554620
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
  3. NM_001428474.1NP_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
  4. NM_001428475.1NP_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
  5. NM_001428476.1NP_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
  6. NM_008053.4NP_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:221280
    KH; K homology RNA-binding domain
    cd00105
    Location:286352
    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:62118
    Agenet; Agenet domain
    pfam12235
    Location:354436
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:462535
    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

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    34074133..34124129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    Q61584
    Conserved Domains (8) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    cd00105
    Location:286352
    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:62117
    Agenet; Agenet domain
    pfam12235
    Location:354465
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:491564
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:583649
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
    pfam17904
    Location:123207
    KH_9; FMRP KH0 domain
    pfam18336
    Location:452
    Tudor_FRX1; Fragile X mental retardation Tudor domain
  2. XM_006535402.2XP_006535465.1  RNA-binding protein FXR1 isoform X4

    Related
    ENSMUSP00000142847.2, ENSMUST00000198051.5
    Conserved Domains (7) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    cd00105
    Location:286352
    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:62117
    Agenet; Agenet domain
    pfam12235
    Location:354465
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:491564
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam17904
    Location:123207
    KH_9; FMRP KH0 domain
    pfam18336
    Location:452
    Tudor_FRX1; Fragile X mental retardation Tudor domain
  3. XM_006535401.2XP_006535464.1  RNA-binding protein FXR1 isoform X2

    UniProtKB/Swiss-Prot
    Q61584
    Conserved Domains (8) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    cd00105
    Location:286352
    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:62117
    Agenet; Agenet domain
    pfam12235
    Location:354436
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:462534
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:581647
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
    pfam17904
    Location:123207
    KH_9; FMRP KH0 domain
    pfam18336
    Location:452
    Tudor_FRX1; Fragile X mental retardation Tudor domain
  4. XM_036162897.1XP_036018790.1  RNA-binding protein FXR1 isoform X6

    UniProtKB/TrEMBL
    A0A0H2UH27
    Conserved Domains (6) summary
    pfam12235
    Location:269380
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:406479
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    cd22504
    Location:38114
    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:133195
    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:196273
    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:141
    Tudor_SF; Tudor domain superfamily
  5. XM_036162895.1XP_036018788.1  RNA-binding protein FXR1 isoform X3

    Conserved Domains (7) summary
    pfam12235
    Location:269380
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:406479
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:525591
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
    cd22504
    Location:38114
    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:133195
    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:196273
    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:141
    Tudor_SF; Tudor domain superfamily
  6. XM_036162896.1XP_036018789.1  RNA-binding protein FXR1 isoform X5

    Conserved Domains (7) summary
    pfam12235
    Location:269380
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:406479
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:498564
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
    cd22504
    Location:38114
    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:133195
    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:196273
    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:141
    Tudor_SF; Tudor domain superfamily