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

    Gene ID: 14359, updated on 18-Sep-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 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
    NEW
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    Try the new Transcript table

    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)

    NEW Try the new Transcript table

    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