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    FMR1 fragile X mental retardation 1 [ Homo sapiens (human) ]

    Gene ID: 2332, updated on 25-Jul-2016
    Official Symbol
    FMR1provided by HGNC
    Official Full Name
    fragile X mental retardation 1provided by HGNC
    Primary source
    HGNC:HGNC:3775
    See related
    Ensembl:ENSG00000102081 HPRD:02398; MIM:309550; Vega:OTTHUMG00000022606
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    POF; FMRP; POF1; FRAXA
    Summary
    The protein encoded by this gene binds RNA and is associated with polysomes. The encoded protein may be involved in mRNA trafficking from the nucleus to the cytoplasm. A trinucleotide repeat (CGG) in the 5' UTR is normally found at 6-53 copies, but an expansion to 55-230 repeats is the cause of fragile X syndrome. Expansion of the trinucleotide repeat may also cause one form of premature ovarian failure (POF1). Multiple alternatively spliced transcript variants that encode different protein isoforms and which are located in different cellular locations have been described for this gene. [provided by RefSeq, May 2010]
    Orthologs
    Location:
    Xq27.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) X NC_000023.11 (147911951..147951127)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (146993469..147032647)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373349 Neighboring gene FMR1 antisense RNA 1 Neighboring gene fragile X mental retardation 1 neighbor Neighboring gene ferritin heavy chain 1 pseudogene 8

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Fragile X syndrome
    MedGen: C0016667 OMIM: 300624 GeneReviews: FMR1-Related Disorders
    Compare labs
    Fragile X tremor/ataxia syndrome
    MedGen: C1839780 OMIM: 300623 GeneReviews: FMR1-Related Disorders
    Compare labs
    Premature ovarian failure 1
    MedGen: C2749126 OMIM: 311360 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-04-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

    ClinGen Genome Curation Page

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag HIV-1 Gag interacts with endogenous fragile X mental retardation protein (FMRP) in an RNase-resistant manner and the NC domain in Gag plays an important role in this interaction PubMed
    capsid gag FMRP is incorporated into HIV-1 particles through association with viral RNP complex including NC, CA, and RT PubMed
    nucleocapsid gag FMRP is incorporated into HIV-1 particles through association with viral RNP complex including NC, CA, and RT PubMed
    gag HIV-1 Gag interacts with endogenous fragile X mental retardation protein (FMRP) in an RNase-resistant manner and the NC domain in Gag plays an important role in this interaction PubMed
    reverse transcriptase gag-pol FMRP is incorporated into HIV-1 particles through association with viral RNP complex including NC, CA, and RT PubMed

    Go to the HIV-1, Human Interaction Database

    • RNA transport, organism-specific biosystem (from KEGG)
      RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    • RNA transport, conserved biosystem (from KEGG)
      RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC87458

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    G-quadruplex RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA stem-loop binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA strand annealing activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    dynein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ion channel binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    mRNA 3'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mRNA 5'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    miRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    microtubule binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    poly(A) RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    poly(G) binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    poly(U) RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ribosome binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sequence-specific mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    siRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    translation initiation factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    translation repressor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to DNA damage stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to UV ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to hydroxyurea ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to virus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    gene silencing by RNA IEA
    Inferred from Electronic Annotation
    more info
     
    glutamate receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    modulation by host of viral RNA genome replication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of cytoplasmic translation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of long term synaptic depression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of synaptic vesicle exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of translation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    negative regulation of translational initiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of voltage-gated calcium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of dendritic spine development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of filopodium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of gene silencing by miRNA IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of histone phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of intracellular transport of viral material IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of proteasomal protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of receptor internalization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of response to DNA damage stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of translation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of alternative mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of dendritic spine development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of filopodium assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of gene silencing by miRNA IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of mRNA stability ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of neuronal action potential IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of neurotransmitter secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    Cajal body IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with SMN complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    axon terminus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    cell projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromocenter ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm TAS
    Traceable Author Statement
    more info
    PubMed 
    cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    dendritic filopodium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    dendritic shaft IEA
    Inferred from Electronic Annotation
    more info
     
    dendritic spine ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    extrinsic component of plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    filopodium tip ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    glial cell projection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    growth cone IDA
    Inferred from Direct Assay
    more info
    PubMed 
    growth cone filopodium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    intracellular ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mRNA cap binding complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuronal ribonucleoprotein granule ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleolus TAS
    Traceable Author Statement
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    perikaryon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perikaryon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with polysomal ribosome TAS
    Traceable Author Statement
    more info
    PubMed 
    polysome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    polysome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    postsynapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    postsynaptic density ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    presynapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    presynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    viral replication complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    synaptic functional regulator FMR1
    Names
    fragile X mental retardation protein 1

    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.

    Genomic

    1. NG_007529.2 RefSeqGene

      Range
      4961..44137
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001185075.1NP_001172004.1  synaptic functional regulator FMR1 isoform ISO6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (ISO6) lacks an alternate segment and uses a different splice site in the 3' coding region which shifts the reading frame, compared to variant ISO1. The resulting protein (isoform ISO6) has a shorter and distinct C-terminus when it is compared to isoform ISO1.
      Source sequence(s)
      BC086957, BQ213316, BX498094, CK825936, L29074
      Consensus CDS
      CCDS55518.1
      UniProtKB/Swiss-Prot
      Q06787
      UniProtKB/TrEMBL
      G8JLE9
      Related
      ENSP00000359502, ENST00000370471
      Conserved Domains (2) summary
      cd00105
      Location:286325
      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:59117
      Agenet; Agenet domain
    2. NM_001185076.1NP_001172005.1  synaptic functional regulator FMR1 isoform ISO7

      See identical proteins and their annotated locations for NP_001172005.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (ISO7) lacks an alternate segment, compared to variant ISO1. The resulting protein (isoform ISO7) is shorter when it is compared to isoform ISO1.
      Source sequence(s)
      BC086957, BQ213316, BQ417290, CN315330, CX871385, L29074
      Consensus CDS
      CCDS55519.1
      UniProtKB/Swiss-Prot
      Q06787
      Related
      ENSP00000218200, ENST00000218200
      Conserved Domains (3) summary
      cd00105
      Location:286325
      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:59117
      Agenet; Agenet domain
      pfam12235
      Location:406488
      FXR1P_C; Fragile X-related 1 protein C terminal
    3. NM_001185081.1NP_001172010.1  synaptic functional regulator FMR1 isoform ISO12

      Status: REVIEWED

      Description
      Transcript Variant: This variant (ISO12) lacks two alternate segments and uses a different splice site which changes the reading frame, compared to variant ISO1. The resulting protein (isoform ISO12) has a shorter and distinct C-terminus when it is compared to isoform ISO1.
      Source sequence(s)
      BC086957, BQ213316, BQ287827, CK825936, L29074
      UniProtKB/Swiss-Prot
      Q06787
      Conserved Domains (2) summary
      cd00105
      Location:286325
      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:59117
      Agenet; Agenet domain
    4. NM_001185082.1NP_001172011.1  synaptic functional regulator FMR1 isoform ISO9

      See identical proteins and their annotated locations for NP_001172011.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (ISO9) lacks an alternate segment and uses a different splice site in the 3' coding region, compared to variant ISO1. The resulting protein (isoform ISO9) is shorter when it is compared to isoform ISO1.
      Source sequence(s)
      BC086957, L29074
      Consensus CDS
      CCDS76039.1
      UniProtKB/Swiss-Prot
      Q06787
      Related
      ENSP00000413764, OTTHUMP00000275550, ENST00000440235, OTTHUMT00000476314
      Conserved Domains (3) summary
      cd00105
      Location:286325
      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:59117
      Agenet; Agenet domain
      pfam12235
      Location:406531
      FXR1P_C; Fragile X-related 1 protein C terminal
    5. NM_002024.5NP_002015.1  synaptic functional regulator FMR1 isoform ISO1

      See identical proteins and their annotated locations for NP_002015.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (ISO1) represents the longest transcript and it encodes the longest protein (isoform ISO1).
      Source sequence(s)
      BC086957, L29074, X69962
      Consensus CDS
      CCDS14682.1
      UniProtKB/Swiss-Prot
      Q06787
      Related
      ENSP00000359506, OTTHUMP00000024197, ENST00000370475, OTTHUMT00000058655
      Conserved Domains (3) summary
      cd00105
      Location:286325
      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:59117
      Agenet; Agenet domain
      pfam12235
      Location:427509
      FXR1P_C; Fragile X-related 1 protein C terminal

    RNA

    1. NR_033699.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (ISO4) lacks an alternate segment, compared to variant ISO1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant ISO1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC086957, BQ213316, BX498094, CK825936, L29074
    2. NR_033700.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (ISO10) lacks two alternate segments, compared to variant ISO1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant ISO1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC086957, BQ213316, CK825936, L29074

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p7 Primary Assembly

      Range
      147911951..147951127
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018934.2 Alternate CHM1_1.1

      Range
      146904323..146943501
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)