Human Gene FRG1 (ENST00000226798.9_5) from GENCODE V47lift37
  Description: FSHD region gene 1 (from RefSeq NM_004477.3)
Gencode Transcript: ENST00000226798.9_5
Gencode Gene: ENSG00000109536.13_14
Transcript (Including UTRs)
   Position: hg19 chr4:190,862,027-190,884,347 Size: 22,321 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr4:190,862,165-190,884,284 Size: 22,120 Coding Exon Count: 9 

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 (chr4:190,862,027-190,884,347)mRNA (may differ from genome)Protein (258 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FRG1_HUMAN
DESCRIPTION: RecName: Full=Protein FRG1; AltName: Full=FSHD region gene 1 protein;
FUNCTION: May have a role in processing of pre-rRNA or in the assembly of rRNA into ribosomal subunits. May be involved in pre- mRNA splicing.
SUBUNIT: Identified in the spliceosome C complex.
SUBCELLULAR LOCATION: Nucleus, Cajal body. Nucleus speckle. Nucleus, nucleolus. Note=First expressed in Cajal bodies and nuclear speckles. As speckle expression diminishes, expression is seen in dense structures (dense fibrillar component and the granular component) of the nucleolus.
TISSUE SPECIFICITY: Expressed in adult muscle, lymphocytes, fetal brain, muscle, and placenta.
SIMILARITY: Belongs to the FRG1 family.

-  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: FRG1
Diseases sorted by gene-association score: facioscapulohumeral muscular dystrophy 1* (32), suppurative lymphadenitis (17), muscular dystrophy (14)
* = Manually curated disease association

-  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: 27.48 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 667.06 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 -35.20138-0.255 Picture PostScript Text
3' UTR -11.5063-0.183 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
IPR008999 - Actin_cross-linking
IPR010414 - FRG1

Pfam Domains:
PF06229 - FRG1-like domain
PF06268 - Fascin domain

SCOP Domains:
50353 - Cytokine
50405 - Actin-crosslinking proteins

ModBase Predicted Comparative 3D Structure on Q14331
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003779 actin binding
GO:0005515 protein binding
GO:0051015 actin filament binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006364 rRNA processing
GO:0006397 mRNA processing
GO:0007517 muscle organ development
GO:0008380 RNA splicing
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0015030 Cajal body
GO:0030018 Z disc
GO:0055120 striated muscle dense body
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  L76159 - Homo sapiens FRG1 mRNA, complete cds.
AK291890 - Homo sapiens cDNA FLJ75747 complete cds, highly similar to Homo sapiens FSHD region gene 1 (FRG1), mRNA.
BC053997 - Homo sapiens FSHD region gene 1, mRNA (cDNA clone MGC:61487 IMAGE:5555121), complete cds.
JD169942 - Sequence 150966 from Patent EP1572962.
CU691066 - Synthetic construct Homo sapiens gateway clone IMAGE:100021599 5' read FRG1 mRNA.
HQ448060 - Synthetic construct Homo sapiens clone IMAGE:100071439; CCSB011885_02 FSHD region gene 1 (FRG1) gene, encodes complete protein.
KJ891197 - Synthetic construct Homo sapiens clone ccsbBroadEn_00591 FRG1 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K775, ENST00000226798.1, ENST00000226798.2, ENST00000226798.3, ENST00000226798.4, ENST00000226798.5, ENST00000226798.6, ENST00000226798.7, ENST00000226798.8, FRG1 , FRG1_HUMAN, NM_004477, Q14331, uc317dmc.1, uc317dmc.2
UCSC ID: ENST00000226798.9_5
RefSeq Accession: NM_004477.3
Protein: Q14331 (aka FRG1_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.