Human Gene FXR2 (ENST00000250113.12_7) from GENCODE V47lift37
  Description: FMR1 autosomal homolog 2 (from RefSeq NM_004860.4)
Gencode Transcript: ENST00000250113.12_7
Gencode Gene: ENSG00000129245.13_10
Transcript (Including UTRs)
   Position: hg19 chr17:7,494,548-7,518,215 Size: 23,668 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr17:7,495,148-7,517,850 Size: 22,703 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:7,494,548-7,518,215)mRNA (may differ from genome)Protein (673 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: FXR2_HUMAN
DESCRIPTION: RecName: Full=Fragile X mental retardation syndrome-related protein 2;
FUNCTION: RNA-binding protein.
SUBUNIT: Interacts with FMR1 and FXR1. Interacts with CYFIP2 but not with CYFIP1. Interacts with TDRD3.
INTERACTION: Q15041:ARL6IP1; NbExp=3; IntAct=EBI-740459, EBI-714543; Q9UIC8:LCMT1; NbExp=2; IntAct=EBI-740459, EBI-747632; O95751:LDOC1; NbExp=3; IntAct=EBI-740459, EBI-740738; Q9NS73:MBIP; NbExp=3; IntAct=EBI-740459, EBI-741953; Q9HAF1:MEAF6; NbExp=3; IntAct=EBI-740459, EBI-399266; P49902:NT5C2; NbExp=3; IntAct=EBI-740459, EBI-742084; P22234:PAICS; NbExp=3; IntAct=EBI-740459, EBI-712261; Q9UI14:RABAC1; NbExp=3; IntAct=EBI-740459, EBI-712367;
SUBCELLULAR LOCATION: Cytoplasm.
DOMAIN: The tandem Tudor domains preferentially recognize trimethylated histone peptides.
SIMILARITY: Belongs to the FMR1 family.
SIMILARITY: Contains 2 Agenet-like domains.
SIMILARITY: Contains 2 KH domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: FXR2
Diseases sorted by gene-association score: fragile x syndrome (10), x-linked disease (2), specific developmental disorder (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 43.89 RPKM in Muscle - Skeletal
Total median expression: 1068.16 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 -219.20365-0.601 Picture PostScript Text
3' UTR -238.90600-0.398 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
PF17904 - FMRP KH0 domain
PF18336 - Fragile X mental retardation Tudor domain

SCOP Domains:
54160 - Chromo domain-like
50044 - SH3-domain
63748 - Tudor/PWWP/MBT
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
3H8Z - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P51116
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0017148 negative regulation of translation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005844 polysome
GO:0016020 membrane
GO:0022625 cytosolic large ribosomal subunit


-  Descriptions from all associated GenBank mRNAs
  AK226082 - Homo sapiens mRNA for fragile X mental retardation syndrome related protein 2 variant, clone: bm00923.
U31501 - Human fragile X mental retardation syndrome related protein (FXR2) mRNA, complete cds.
BC067272 - Homo sapiens fragile X mental retardation, autosomal homolog 2, mRNA (cDNA clone MGC:75052 IMAGE:6204341), complete cds.
BC051907 - Homo sapiens fragile X mental retardation, autosomal homolog 2, mRNA (cDNA clone MGC:60375 IMAGE:6149976), complete cds.
BC020090 - Homo sapiens fragile X mental retardation, autosomal homolog 2, mRNA (cDNA clone MGC:21187 IMAGE:4385430), complete cds.
JD531206 - Sequence 512230 from Patent EP1572962.
JD219014 - Sequence 200038 from Patent EP1572962.
JD223066 - Sequence 204090 from Patent EP1572962.
JD181835 - Sequence 162859 from Patent EP1572962.
JD331487 - Sequence 312511 from Patent EP1572962.
JD485582 - Sequence 466606 from Patent EP1572962.
JD077525 - Sequence 58549 from Patent EP1572962.
JD279997 - Sequence 261021 from Patent EP1572962.
JD123023 - Sequence 104047 from Patent EP1572962.
JD124346 - Sequence 105370 from Patent EP1572962.
JD095682 - Sequence 76706 from Patent EP1572962.
JD155689 - Sequence 136713 from Patent EP1572962.
JD322523 - Sequence 303547 from Patent EP1572962.
JD148722 - Sequence 129746 from Patent EP1572962.
JD306779 - Sequence 287803 from Patent EP1572962.
AK313836 - Homo sapiens cDNA, FLJ94461, highly similar to Homo sapiens fragile X mental retardation, autosomal homolog 2 (FXR2), mRNA.
BT009817 - Homo sapiens fragile X mental retardation, autosomal homolog 2 mRNA, complete cds.
KJ892786 - Synthetic construct Homo sapiens clone ccsbBroadEn_02180 FXR2 gene, encodes complete protein.
KJ898040 - Synthetic construct Homo sapiens clone ccsbBroadEn_07434 FXR2 gene, encodes complete protein.
CU676498 - Synthetic construct Homo sapiens gateway clone IMAGE:100017448 5' read FXR2 mRNA.
CU690884 - Synthetic construct Homo sapiens gateway clone IMAGE:100021474 5' read FXR2 mRNA.
JD150423 - Sequence 131447 from Patent EP1572962.
JD142249 - Sequence 123273 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9M2, D3DTQ1, ENST00000250113.1, ENST00000250113.10, ENST00000250113.11, ENST00000250113.2, ENST00000250113.3, ENST00000250113.4, ENST00000250113.5, ENST00000250113.6, ENST00000250113.7, ENST00000250113.8, ENST00000250113.9, FMR1L2, FXR2 , FXR2_HUMAN, NM_004860, P51116, Q86V09, Q8WUM2, uc317fay.1, uc317fay.2
UCSC ID: ENST00000250113.12_7
RefSeq Accession: NM_004860.4
Protein: P51116 (aka FXR2_HUMAN)

-  Gene Model Information
  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.