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Fxr1 fragile X mental retardation gene 1, autosomal homolog [ Mus musculus (house mouse) ]

Gene ID: 14359, updated on 10-Oct-2019

Summary

Official Symbol
Fxr1provided by MGI
Official Full Name
fragile X mental retardation gene 1, autosomal homologprovided by MGI
Primary source
MGI:MGI:104860
See related
Ensembl:ENSMUSG00000027680
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; AI851072; 1110050J02Rik; 9530073J07Rik
Expression
Broad expression in testis adult (RPKM 55.6), CNS E11.5 (RPKM 32.4) and 20 other tissues See more
Orthologs

Genomic context

See Fxr1 in Genome Data Viewer
Location:
3; 3 A3
Exon count:
17
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (34020058..34069980)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (33919001..33968267)

Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene calcium regulated heat stable protein 1 pseudogene Neighboring gene predicted gene, 46798 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 Neighboring gene SET translocation pseudogene Neighboring gene uncharacterized LOC115489717

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 BioSystems

  • 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) ...
  • mRNA processing, organism-specific biosystem (from WikiPathways)
    mRNA processing, organism-specific biosystemAdapted from Reactome, see: [http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1675.1 REACT 1675.1] This process describes the conversion of precursor messenger RNA into mature messenge...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
G-quadruplex RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
NOT G-quadruplex RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA strand annealing activity ISO
Inferred from Sequence Orthology
more info
 
mRNA 3'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
protein homodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
translation regulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
muscle organ development IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene silencing by miRNA ISO
Inferred from Sequence Orthology
more info
 
positive regulation of protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of response to DNA damage stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of filopodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of mRNA stability IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of translation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon IDA
Inferred from Direct Assay
more info
PubMed 
costamere IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol ISO
Inferred from Sequence Orthology
more info
 
dendrite IDA
Inferred from Direct Assay
more info
PubMed 
dendritic filopodium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic spine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic spine IDA
Inferred from Direct Assay
more info
PubMed 
dendritic spine neck IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
growth cone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
polysome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
polysome IDA
Inferred from Direct Assay
more info
PubMed 
postsynapse IDA
Inferred from Direct Assay
more info
PubMed 
postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
presynapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
fragile X mental retardation syndrome-related protein 1
Names
fragile X mental retardation gene, autosomal homolog

NCBI Reference Sequences (RefSeq)

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_001113188.1NP_001106659.1  fragile X mental retardation syndrome-related protein 1 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)
    AA080092, BE634703, CB196254, CJ086949, X90875
    Consensus CDS
    CCDS50891.1
    UniProtKB/Swiss-Prot
    Q61584
    Related
    ENSMUSP00000001620.8, ENSMUST00000001620.12
    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_001113189.1NP_001106660.1  fragile X mental retardation syndrome-related protein 1 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)
    BE634703, CF170707, CJ086949, X90875
    Consensus CDS
    CCDS79896.1
    UniProtKB/Swiss-Prot
    Q61584
    Related
    ENSMUSP00000142441.1, ENSMUST00000197694.4
    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_008053.2NP_032079.1  fragile X mental retardation syndrome-related protein 1 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)
    BE634703, CJ086949, X90875
    Consensus CDS
    CCDS50890.1
    UniProtKB/Swiss-Prot
    Q61584
    Related
    ENSMUSP00000143392.1, ENSMUST00000200392.4
    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 108 details...Open this link in a new tab

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

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000069.6 Reference GRCm38.p6 C57BL/6J

    Range
    34020058..34069980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006535400.1XP_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 (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: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
  2. XM_006535402.1XP_006535465.1  fragile X mental retardation syndrome-related protein 1 isoform X3

    See identical proteins and their annotated locations for XP_006535465.1

    UniProtKB/Swiss-Prot
    Q61584
    UniProtKB/TrEMBL
    A0A0G2JEP0
    Related
    ENSMUSP00000142847.1, ENSMUST00000198051.4
    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: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
  3. XM_006535401.1XP_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 (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: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
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