Human Gene FXR1 (uc003fkq.3)
  Description: Homo sapiens fragile X mental retardation, autosomal homolog 1 (FXR1), transcript variant 1, mRNA.
RefSeq Summary (NM_005087): 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].
Transcript (Including UTRs)
   Position: hg19 chr3:180,630,234-180,700,539 Size: 70,306 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr3:180,630,474-180,694,080 Size: 63,607 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:180,630,234-180,700,539)mRNA (may differ from genome)Protein (621 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSCGAPEnsemblEntrez GeneExonPrimer
GeneCardsGeneNetworkH-INVHGNCHPRDLynx
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: FXR1_HUMAN
DESCRIPTION: RecName: Full=Fragile X mental retardation syndrome-related protein 1; Short=hFXR1p;
FUNCTION: RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs (By similarity).
SUBUNIT: Interacts with FMR1 and FXR2. Interacts with TDRD3, and with CYFIP2 but not with CYFIP1.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Expressed in all tissues examined including heart, brain, kidney and testis.
DOMAIN: The tandem Tudor domains preferentially recognize trimethylated histone peptides.
PTM: Arg-445 is dimethylated, probably to asymmetric dimethylarginine.
SIMILARITY: Belongs to the FMR1 family.
SIMILARITY: Contains 2 Agenet-like domains.
SIMILARITY: Contains 2 KH domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FXR1
CDC HuGE Published Literature: FXR1
Positive Disease Associations: Gallbladder Diseases , schizophrenia
Related Studies:
  1. Gallbladder Diseases
    , , . [PubMed 0]
  2. schizophrenia
    International Schizophrenia Consortium ,et al. 2009, Common polygenic variation contributes to risk of schizophrenia and bipolar disorder, Nature 2009 460- 7256 : 748-52. [PubMed 19571811]

-  MalaCards Disease Associations
  MalaCards Gene Search: FXR1
Diseases sorted by gene-association score: fragile x syndrome (9), x-linked disease (2), specific developmental disorder (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 45.58 RPKM in Muscle - Skeletal
Total median expression: 532.33 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -92.00240-0.383 Picture PostScript Text
3' UTR -1626.456459-0.252 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008395 - Agenet-like_dom
IPR022034 - Frag_X_MRP_fam
IPR004087 - KH_dom
IPR004088 - KH_dom_type_1

Pfam Domains:
PF00013 - KH domain
PF05641 - Agenet domain
PF12235 - Fragile X-related 1 protein core C terminal
PF16096 - Fragile X-related 1 protein C-terminal region 2
PF16097 - Fragile X-related 1 protein C-terminal region 3

SCOP Domains:
54791 - Eukaryotic type KH-domain (KH-domain type I)
54814 - Prokaryotic type KH domain (KH-domain type II)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2CPQ - NMR MuPIT 3KUF - X-ray MuPIT 3O8V - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P51114
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002151 G-quadruplex RNA binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0033592 RNA strand annealing activity
GO:0042803 protein homodimerization activity
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006915 apoptotic process
GO:0007275 multicellular organism development
GO:0007517 muscle organ development
GO:0017148 negative regulation of translation
GO:0030154 cell differentiation
GO:2000637 positive regulation of gene silencing by miRNA

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005844 polysome
GO:0016020 membrane
GO:0030424 axon
GO:0030425 dendrite
GO:0035770 ribonucleoprotein granule
GO:0043034 costamere
GO:0043197 dendritic spine
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  KJ895659 - Synthetic construct Homo sapiens clone ccsbBroadEn_05053 TTC14 gene, encodes complete protein.
MF125244 - Homo sapiens bio-material 4-09KM0664 case FXR1/MYC fusion mRNA, partial sequence.
BC010382 - Homo sapiens fragile X mental retardation, autosomal homolog 1, mRNA (cDNA clone IMAGE:4080296), with apparent retained intron.
AK297254 - Homo sapiens cDNA FLJ58021 complete cds, highly similar to Fragile X mental retardation syndrome-related protein 1.
AK294603 - Homo sapiens cDNA FLJ58772 complete cds, highly similar to Fragile X mental retardation syndrome-related protein 1.
AK297331 - Homo sapiens cDNA FLJ58199 complete cds, highly similar to Fragile X mental retardation syndrome-related protein 1.
AK292633 - Homo sapiens cDNA FLJ75450 complete cds, highly similar to Homo sapiens fragile X mental retardation, autosomal homolog 1(FXR1), mRNA.
AK225334 - Homo sapiens mRNA for fragile X mental retardation-related protein 1 isoform b variant, clone: HEP08305.
U25165 - Human fragile X mental retardation protein 1 homolog FXR1 mRNA, complete cds.
BC028983 - Homo sapiens fragile X mental retardation, autosomal homolog 1, mRNA (cDNA clone MGC:29858 IMAGE:5122574), complete cds.
AM393164 - Synthetic construct Homo sapiens clone IMAGE:100002624 for hypothetical protein (FXR1 gene).
AM393496 - Synthetic construct Homo sapiens clone IMAGE:100002625 for hypothetical protein (FXR1 gene).
AM393057 - Synthetic construct Homo sapiens clone IMAGE:100002894 for hypothetical protein (FXR1 gene).
AB463046 - Synthetic construct DNA, clone: pF1KB8707, Homo sapiens FXR1 gene for fragile X mental retardation, autosomal homolog 1, without stop codon, in Flexi system.
KR259877 - Homo sapiens fragile X mental retardation autosomal homolog variant p4K (FXR1) mRNA, complete cds, alternatively spliced.
KR259878 - Homo sapiens fragile X mental retardation autosomal homolog variant p2K (FXR1) mRNA, complete cds, alternatively spliced.
KR259879 - Homo sapiens fragile X mental retardation autosomal homolog variant p5FK (FXR1) mRNA, complete cds, alternatively spliced.
KR259880 - Homo sapiens fragile X mental retardation autosomal homolog variant p1K (FXR1) mRNA, complete cds, alternatively spliced.
AY341428 - Homo sapiens fragile X mental retardation autosomal homolog 1-like protein mRNA, complete cds; alternatively spliced.
AK302197 - Homo sapiens cDNA FLJ58644 complete cds, highly similar to Fragile X mental retardation syndrome-related protein 1.
LF206097 - JP 2014500723-A/13600: Polycomb-Associated Non-Coding RNAs.
X90874 - H.sapiens mRNA for FXR1 protein.
LF351339 - JP 2014500723-A/158842: Polycomb-Associated Non-Coding RNAs.
LF351343 - JP 2014500723-A/158846: Polycomb-Associated Non-Coding RNAs.
LF351344 - JP 2014500723-A/158847: Polycomb-Associated Non-Coding RNAs.
LF351345 - JP 2014500723-A/158848: Polycomb-Associated Non-Coding RNAs.
LF351352 - JP 2014500723-A/158855: Polycomb-Associated Non-Coding RNAs.
LF351353 - JP 2014500723-A/158856: Polycomb-Associated Non-Coding RNAs.
JD171088 - Sequence 152112 from Patent EP1572962.
LF351354 - JP 2014500723-A/158857: Polycomb-Associated Non-Coding RNAs.
JD504448 - Sequence 485472 from Patent EP1572962.
JD522825 - Sequence 503849 from Patent EP1572962.
LF351355 - JP 2014500723-A/158858: Polycomb-Associated Non-Coding RNAs.
JD084970 - Sequence 65994 from Patent EP1572962.
LF351356 - JP 2014500723-A/158859: Polycomb-Associated Non-Coding RNAs.
LF351357 - JP 2014500723-A/158860: Polycomb-Associated Non-Coding RNAs.
AF075028 - Homo sapiens full length insert cDNA YI38B04.
LF351358 - JP 2014500723-A/158861: Polycomb-Associated Non-Coding RNAs.
MA586916 - JP 2018138019-A/158842: Polycomb-Associated Non-Coding RNAs.
MA586920 - JP 2018138019-A/158846: Polycomb-Associated Non-Coding RNAs.
MA586921 - JP 2018138019-A/158847: Polycomb-Associated Non-Coding RNAs.
MA586922 - JP 2018138019-A/158848: Polycomb-Associated Non-Coding RNAs.
MA586929 - JP 2018138019-A/158855: Polycomb-Associated Non-Coding RNAs.
MA586930 - JP 2018138019-A/158856: Polycomb-Associated Non-Coding RNAs.
MA586931 - JP 2018138019-A/158857: Polycomb-Associated Non-Coding RNAs.
MA586932 - JP 2018138019-A/158858: Polycomb-Associated Non-Coding RNAs.
MA586933 - JP 2018138019-A/158859: Polycomb-Associated Non-Coding RNAs.
MA586934 - JP 2018138019-A/158860: Polycomb-Associated Non-Coding RNAs.
MA586935 - JP 2018138019-A/158861: Polycomb-Associated Non-Coding RNAs.
MA441674 - JP 2018138019-A/13600: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P51114 (Reactome details) participates in the following event(s):

R-HSA-6802927 BRAF and RAF fusion mutant dimers are phosphorylated
R-HSA-6802934 p-BRAF and RAF fusion dimers bind MAP2Ks and MAPKs
R-HSA-6802932 Dissociation of BRAF/RAF fusion complex
R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks
R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers
R-HSA-6802952 Signaling by BRAF and RAF fusions
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9B8, FXR1_HUMAN, NM_005087, NP_001013457, P51114, Q7Z450, Q8N6R8
UCSC ID: uc003fkq.3
RefSeq Accession: NM_005087
Protein: P51114 (aka FXR1_HUMAN)
CCDS: CCDS3238.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005087.3
exon count: 17CDS single in 3' UTR: no RNA size: 8567
ORF size: 1866CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3614.00frame shift in genome: no % Coverage: 99.98
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.