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FXR1 FMR1 autosomal homolog 1 [ Homo sapiens (human) ]

Gene ID: 8087, updated on 9-Sep-2018

Summary

Official Symbol
FXR1provided by HGNC
Official Full Name
FMR1 autosomal homolog 1provided by HGNC
Primary source
HGNC:HGNC:4023
See related
Ensembl:ENSG00000114416 MIM:600819; Vega:OTTHUMG00000158138
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
FXR1P
Summary
The protein encoded by this gene is an RNA binding protein that interacts with the functionally-similar proteins FMR1 and FXR2. These proteins shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 27.2), ovary (RPKM 11.8) and 25 other tissues See more
Orthologs

Genomic context

See FXR1 in Genome Data Viewer
Location:
3q26.33
Exon count:
19
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (180912446..180982753)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (180630096..180700541)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928882 Neighboring gene uncharacterized LOC105374240 Neighboring gene ribosomal protein L32 pseudogene 10 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 Neighboring gene VISTA enhancer hs192 Neighboring gene SOX2 overlapping transcript

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of fragile X mental retardation, autosomal homolog 1 (FXR1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Interaction of HIV-1 Gag with fragile X mental retardation, autosomal homolog 1 (FXR1) is identified in a series of six affinity purification/mass spectrometry screens PubMed
Tat tat Fragile X mental retardation, autosomal homolog 1 (FXR1) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
    Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
  • Oncogenic MAPK signaling, organism-specific biosystem (from REACTOME)
    Oncogenic MAPK signaling, organism-specific biosystemThe importance of the RAS/RAF/MAPK cascade in regulating cellular proliferation, differentiation and survival is highlighted by the fact that components of the pathway are mutated with high frequency...
  • 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) ...
  • Signaling by BRAF and RAF fusions, organism-specific biosystem (from REACTOME)
    Signaling by BRAF and RAF fusions, organism-specific biosystemIn addition to the more prevalent point mutations, BRAF and RAF1 are also subject to activation as a result of translocation events that yield truncated or fusion products (Jones et al, 2008; Cin et ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
G-quadruplex RNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
RNA strand annealing activity IDA
Inferred from Direct Assay
more info
PubMed 
mRNA 3'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 3'-UTR binding IEA
Inferred from Electronic Annotation
more info
 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
translation regulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
apoptotic process TAS
Traceable Author Statement
more info
PubMed 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
muscle organ development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of translation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene silencing by miRNA IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of mRNA stability IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon IEA
Inferred from Electronic Annotation
more info
 
costamere IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasmic ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
dendritic spine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic spine IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleolus TAS
Traceable Author Statement
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
polysome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein granule IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

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_001013438.2NP_001013456.1  fragile X mental retardation syndrome-related protein 1 isoform b

    See identical proteins and their annotated locations for NP_001013456.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC008009, AK225334, DC352767
    Consensus CDS
    CCDS46965.1
    UniProtKB/Swiss-Prot
    P51114
    Related
    ENSP00000388828.2, OTTHUMP00000212643, ENST00000445140.6, OTTHUMT00000350269
    Conserved Domains (5) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:286352
    KH_1; KH domain
    pfam05641
    Location:62117
    Agenet; Agenet domain
    pfam12235
    Location:354438
    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
  2. NM_001013439.2NP_001013457.1  fragile X mental retardation syndrome-related protein 1 isoform c

    See identical proteins and their annotated locations for NP_001013457.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
    Source sequence(s)
    AC008009, AK292633, AU280585, DC352767
    Consensus CDS
    CCDS33894.1
    UniProtKB/Swiss-Prot
    P51114
    Related
    ENSP00000307633.7, OTTHUMP00000212644, ENST00000305586.11, OTTHUMT00000350271
    Conserved Domains (5) summary
    smart00322
    Location:136195
    KH; K homology RNA-binding domain
    pfam00013
    Location:201267
    KH_1; KH domain
    pfam12235
    Location:269353
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:377450
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:469535
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
  3. NM_001363882.1NP_001350811.1  fragile X mental retardation syndrome-related protein 1 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC008009
    Consensus CDS
    CCDS87169.1
    Conserved Domains (4) summary
    smart00322
    Location:136195
    KH; K homology RNA-binding domain
    pfam00013
    Location:201267
    KH_1; KH domain
    pfam12235
    Location:269353
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:377450
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
  4. NM_005087.3NP_005078.2  fragile X mental retardation syndrome-related protein 1 isoform a

    See identical proteins and their annotated locations for NP_005078.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC008009, AK292633, DC352767
    Consensus CDS
    CCDS3238.1
    UniProtKB/Swiss-Prot
    P51114
    Related
    ENSP00000350170.3, OTTHUMP00000212640, ENST00000357559.8, OTTHUMT00000350265
    Conserved Domains (6) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:286352
    KH_1; KH domain
    pfam05641
    Location:62117
    Agenet; Agenet domain
    pfam12235
    Location:354438
    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

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    180912446..180982753
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005247813.3XP_005247870.2  fragile X mental retardation syndrome-related protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005247870.2

    UniProtKB/TrEMBL
    A0A0F7KYT8
    Conserved Domains (6) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:286352
    KH_1; KH domain
    pfam05641
    Location:62117
    Agenet; Agenet domain
    pfam12235
    Location:354467
    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. XM_005247814.3XP_005247871.2  fragile X mental retardation syndrome-related protein 1 isoform X2

    See identical proteins and their annotated locations for XP_005247871.2

    Conserved Domains (6) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:286352
    KH_1; KH domain
    pfam05641
    Location:62117
    Agenet; Agenet domain
    pfam12235
    Location:354467
    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
  3. XM_005247816.3XP_005247873.2  fragile X mental retardation syndrome-related protein 1 isoform X4

    See identical proteins and their annotated locations for XP_005247873.2

    Related
    ENSP00000420643.1, OTTHUMP00000212641, ENST00000491062.5, OTTHUMT00000350267
    Conserved Domains (5) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:286352
    KH_1; KH domain
    pfam05641
    Location:62117
    Agenet; Agenet domain
    pfam12235
    Location:354467
    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
  4. XM_005247815.3XP_005247872.2  fragile X mental retardation syndrome-related protein 1 isoform X3

    See identical proteins and their annotated locations for XP_005247872.2

    UniProtKB/TrEMBL
    A0A0F7L1S3
    Related
    ENSP00000418097.1, OTTHUMP00000212645, ENST00000480918.5, OTTHUMT00000350272
    Conserved Domains (6) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:286352
    KH_1; KH domain
    pfam05641
    Location:62117
    Agenet; Agenet domain
    pfam12235
    Location:354438
    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
  5. XM_006713775.3XP_006713838.1  fragile X mental retardation syndrome-related protein 1 isoform X5

    See identical proteins and their annotated locations for XP_006713838.1

    Conserved Domains (5) summary
    smart00322
    Location:136195
    KH; K homology RNA-binding domain
    cd00105
    Location:201267
    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 ...
    pfam12235
    Location:269380
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:406478
    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
  6. XM_017007299.1XP_016862788.1  fragile X mental retardation syndrome-related protein 1 isoform X7

    Conserved Domains (5) summary
    smart00322
    Location:136195
    KH; K homology RNA-binding domain
    cd00105
    Location:201267
    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 ...
    pfam12235
    Location:269351
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:377449
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
    pfam16097
    Location:496562
    FXR_C3; Fragile X-related 1 protein C-terminal region 3
  7. XM_017007300.1XP_016862789.1  fragile X mental retardation syndrome-related protein 1 isoform X8

    Conserved Domains (4) summary
    smart00322
    Location:136195
    KH; K homology RNA-binding domain
    cd00105
    Location:201267
    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 ...
    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
  8. XM_017007301.1XP_016862790.1  fragile X mental retardation syndrome-related protein 1 isoform X9

    UniProtKB/TrEMBL
    E7EU85
    Related
    ENSP00000420515.1, OTTHUMP00000212642, ENST00000468861.5, OTTHUMT00000350268
    Conserved Domains (4) summary
    smart00322
    Location:136195
    KH; K homology RNA-binding domain
    pfam00013
    Location:201267
    KH_1; KH domain
    pfam12235
    Location:269353
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16096
    Location:377450
    FXR_C1; Fragile X-related 1 protein C-terminal region 2
  9. XM_017007298.2XP_016862787.1  fragile X mental retardation syndrome-related protein 1 isoform X6

    Conserved Domains (5) summary
    smart00322
    Location:136195
    KH; K homology RNA-binding domain
    cd00105
    Location:201267
    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 ...
    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

RNA

  1. XR_002959596.1 RNA Sequence

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