Human Gene FCHSD2 (uc009ytl.3)
  Description: Homo sapiens FCH and double SH3 domains 2 (FCHSD2), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr11:72,547,790-72,853,143 Size: 305,354 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr11:72,549,836-72,852,922 Size: 303,087 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:72,547,790-72,853,143)mRNA (may differ from genome)Protein (740 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FCSD2_HUMAN
DESCRIPTION: RecName: Full=FCH and double SH3 domains protein 2; AltName: Full=Carom; AltName: Full=SH3 multiple domains protein 3;
SUBUNIT: Interacts with CASK and MAGI1. CASK inhibits interaction with MAGI1.
INTERACTION: Q62915:Cask (xeno); NbExp=2; IntAct=EBI-1215612, EBI-704635; Q96QZ7:MAGI1; NbExp=5; IntAct=EBI-1215612, EBI-924464; P55072:VCP; NbExp=2; IntAct=EBI-1215612, EBI-355164;
TISSUE SPECIFICITY: Liver, brain, heart, placenta, skeletal muscle, pancreas, lung and kidney.
SIMILARITY: Contains 1 FCH domain.
SIMILARITY: Contains 2 SH3 domains.
SEQUENCE CAUTION: Sequence=BAA34489.2; Type=Erroneous initiation;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FCHSD2
CDC HuGE Published Literature: FCHSD2

-  MalaCards Disease Associations
  MalaCards Gene Search: FCHSD2
Diseases sorted by gene-association score: deafness, autosomal recessive 63 (2)

-  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: 29.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 539.07 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 -73.44221-0.332 Picture PostScript Text
3' UTR -613.332046-0.300 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
IPR001060 - FCH
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00611 - Fes/CIP4, and EFC/F-BAR homology domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
50044 - SH3-domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DL5 - NMR MuPIT 2DL7 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O94868
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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 orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007274 neuromuscular synaptic transmission
GO:0030833 regulation of actin filament polymerization

Cellular Component:
GO:0031594 neuromuscular junction
GO:0055037 recycling endosome


-  Descriptions from all associated GenBank mRNAs
  AL133567 - Homo sapiens mRNA; cDNA DKFZp434L127 (from clone DKFZp434L127).
AB018312 - Homo sapiens mRNA for KIAA0769 protein, partial cds.
AK297928 - Homo sapiens cDNA FLJ56467 complete cds, highly similar to Homo sapiens FCH and double SH3 domains 2 (FCHSD2), mRNA.
AK296376 - Homo sapiens cDNA FLJ60613 complete cds, highly similar to Mus musculus FCH and double SH3 domains 2 (Fchsd2), mRNA.
AB383983 - Synthetic construct DNA, clone: pF1KSDA0769, Homo sapiens FCHSD2 gene for FCH and double SH3 domains protein 2, complete cds, without stop codon, in Flexi system.
BC010394 - Homo sapiens FCH and double SH3 domains 2, mRNA (cDNA clone MGC:13671 IMAGE:4091973), complete cds.
JF432171 - Synthetic construct Homo sapiens clone IMAGE:100073325 FCH and double SH3 domains 2 (FCHSD2) gene, encodes complete protein.
KJ902033 - Synthetic construct Homo sapiens clone ccsbBroadEn_11427 FCHSD2 gene, encodes complete protein.
CU679693 - Synthetic construct Homo sapiens gateway clone IMAGE:100019751 5' read FCHSD2 mRNA.
LF207797 - JP 2014500723-A/15300: Polycomb-Associated Non-Coding RNAs.
AL080236 - Homo sapiens mRNA; cDNA DKFZp586M2421 (from clone DKFZp586M2421).
BC017751 - Homo sapiens FCH and double SH3 domains 2, mRNA (cDNA clone IMAGE:4425994), partial cds.
JD256383 - Sequence 237407 from Patent EP1572962.
JD098777 - Sequence 79801 from Patent EP1572962.
LF369270 - JP 2014500723-A/176773: Polycomb-Associated Non-Coding RNAs.
LF369269 - JP 2014500723-A/176772: Polycomb-Associated Non-Coding RNAs.
AK128381 - Homo sapiens cDNA FLJ46524 fis, clone THYMU3034453.
JD263277 - Sequence 244301 from Patent EP1572962.
JD450210 - Sequence 431234 from Patent EP1572962.
JD477716 - Sequence 458740 from Patent EP1572962.
JD450716 - Sequence 431740 from Patent EP1572962.
JD329489 - Sequence 310513 from Patent EP1572962.
JD209912 - Sequence 190936 from Patent EP1572962.
JD230251 - Sequence 211275 from Patent EP1572962.
JD148149 - Sequence 129173 from Patent EP1572962.
JD357864 - Sequence 338888 from Patent EP1572962.
JD299608 - Sequence 280632 from Patent EP1572962.
JD361801 - Sequence 342825 from Patent EP1572962.
JD075504 - Sequence 56528 from Patent EP1572962.
LF369268 - JP 2014500723-A/176771: Polycomb-Associated Non-Coding RNAs.
LF369266 - JP 2014500723-A/176769: Polycomb-Associated Non-Coding RNAs.
LF369265 - JP 2014500723-A/176768: Polycomb-Associated Non-Coding RNAs.
LF369264 - JP 2014500723-A/176767: Polycomb-Associated Non-Coding RNAs.
MA604847 - JP 2018138019-A/176773: Polycomb-Associated Non-Coding RNAs.
MA604846 - JP 2018138019-A/176772: Polycomb-Associated Non-Coding RNAs.
MA604845 - JP 2018138019-A/176771: Polycomb-Associated Non-Coding RNAs.
MA604843 - JP 2018138019-A/176769: Polycomb-Associated Non-Coding RNAs.
MA604842 - JP 2018138019-A/176768: Polycomb-Associated Non-Coding RNAs.
MA604841 - JP 2018138019-A/176767: Polycomb-Associated Non-Coding RNAs.
MA443374 - JP 2018138019-A/15300: Polycomb-Associated Non-Coding RNAs.
JD210861 - Sequence 191885 from Patent EP1572962.
JD520560 - Sequence 501584 from Patent EP1572962.
JD417153 - Sequence 398177 from Patent EP1572962.
JD520402 - Sequence 501426 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DNI3, FCSD2_HUMAN, KIAA0769, NM_014824, NP_055639, O94868, Q7L8J9, Q8WVM2, Q96FV7, Q9UF77, SH3MD3
UCSC ID: uc009ytl.3
RefSeq Accession: NM_014824
Protein: O94868 (aka FCSD2_HUMAN)
CCDS: CCDS8218.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014824.2
exon count: 20CDS single in 3' UTR: no RNA size: 4507
ORF size: 2223CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 4638.00frame shift in genome: no % Coverage: 99.62
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.