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

Gene ID: 14359, updated on 22-Dec-2022

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
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Genomic context

See Fxr1 in Genome Data Viewer
Location:
3; 3 A3
Exon count:
18
Annotation release Status Assembly Chr Location
109 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 predicted gene, 46833 Neighboring gene calcium regulated heat stable protein 1 pseudogene Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 Neighboring gene SET translocation pseudogene Neighboring gene predicted gene, 52623

Genomic regions, transcripts, and products

Expression

  • 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

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

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA strand annealing activity ISO
Inferred from Sequence Orthology
more info
 
enables mRNA 3'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables mRNA binding IEA
Inferred from Electronic Annotation
more info
 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables translation regulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
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 translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of miRNA-mediated gene silencing ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of response to DNA damage stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of filopodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of mRNA stability IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of translation IEA
Inferred from Electronic Annotation
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
 
Component Evidence Code Pubs
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in axon IDA
Inferred from Direct Assay
more info
PubMed 
located_in costamere IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in cytoplasmic ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
is_active_in dendritic filopodium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in dendritic spine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in dendritic spine IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in dendritic spine neck IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in growth cone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
part_of polysome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of polysome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in postsynapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in presynapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
RNA-binding protein FXR1; fragile X mental retardation syndrome-related protein 1

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_001113188.2NP_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, 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_001113189.2NP_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_008053.3NP_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/Swiss-Prot
    Q61584
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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  fragile X mental retardation syndrome-related protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006535463.1

    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  fragile X mental retardation syndrome-related protein 1 isoform X4

    See identical proteins and their annotated locations for XP_006535465.1

    UniProtKB/Swiss-Prot
    Q61584
    UniProtKB/TrEMBL
    A0A0G2JEP0
    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  fragile X mental retardation syndrome-related protein 1 isoform X2

    See identical proteins and their annotated locations for XP_006535464.1

    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  fragile X mental retardation syndrome-related protein 1 isoform X6

    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  fragile X mental retardation syndrome-related protein 1 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  fragile X mental retardation syndrome-related protein 1 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