Human Gene CWC22 (uc010frh.1) Description and Page Index
  Description: Homo sapiens CWC22 spliceosome-associated protein homolog (S. cerevisiae) (CWC22), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:180,809,604-180,871,780 Size: 62,177 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr2:180,809,856-180,858,068 Size: 48,213 Coding Exon Count: 19 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:180,809,604-180,871,780)mRNA (may differ from genome)Protein (908 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CWC22_HUMAN
DESCRIPTION: RecName: Full=Pre-mRNA-splicing factor CWC22 homolog; AltName: Full=Nucampholin homolog; AltName: Full=fSAPb;
FUNCTION: May be involved in pre-mRNA splicing.
SUBUNIT: Component of the spliceosome C complex.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the CWC22 family.
SIMILARITY: Contains 1 MI domain.
SIMILARITY: Contains 1 MIF4G domain.
SEQUENCE CAUTION: Sequence=AAH16651.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH31216.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH57826.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAB13430.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAB15197.1; Type=Frameshift; Positions=555; Sequence=BAB15612.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CWC22
CDC HuGE Published Literature: CWC22
Positive Disease Associations: Asthma , Carotid Arteries , Hematocrit , Hemoglobins , Lupus Erythematosus, Systemic , Myocardial Infarction , Obesity , Prostatic Neoplasms , Stroke
Related Studies:
  1. Asthma
    C Ober et al. American journal of human genetics 2000, A second-generation genomewide screen for asthma-susceptibility alleles in a founder population., American journal of human genetics. [PubMed 11022011]
  2. Carotid Arteries
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.
  3. Hematocrit
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CWC22
Diseases sorted by gene-association score: melanomatosis (3), meningeal melanocytoma (2), meningeal melanomatosis (2), central nervous system melanocytic neoplasm (2)

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 402.34 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -109.70300-0.366 Picture PostScript Text
3' UTR -41.60252-0.165 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
IPR016024 - ARM-type_fold
IPR003891 - Initiation_fac_eIF4g_MI
IPR016021 - MIF4-like_typ_1/2/3
IPR003890 - MIF4G-like_typ-3

Pfam Domains:
PF02847 - MA3 domain

SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q9HCG8
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 Details     
Gene Sorter     
      
      
      

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

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0048024 regulation of mRNA splicing, via spliceosome

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0071006 U2-type catalytic step 1 spliceosome
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AK026978 - Homo sapiens cDNA: FLJ23325 fis, clone HEP12505.
AK123647 - Homo sapiens cDNA FLJ41653 fis, clone FEBRA2024987, weakly similar to Caenorhabditis elegans Nucampholin (let-858).
AB046824 - Homo sapiens KIAA1604 mRNA for KIAA1604 protein.
BC041662 - Homo sapiens, Similar to hypothetical protein B230213M24, clone IMAGE:4996115, mRNA.
BC053573 - Homo sapiens CWC22 spliceosome-associated protein homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3873747), partial cds.
BC143433 - Homo sapiens cDNA clone IMAGE:9051941.
BC093952 - Homo sapiens CWC22 spliceosome-associated protein homolog (S. cerevisiae), mRNA (cDNA clone MGC:120987 IMAGE:7939797), complete cds.
BC093954 - Homo sapiens CWC22 spliceosome-associated protein homolog (S. cerevisiae), mRNA (cDNA clone MGC:120989 IMAGE:7939799), complete cds.
KJ899368 - Synthetic construct Homo sapiens clone ccsbBroadEn_08762 CWC22 gene, encodes complete protein.
AB385487 - Synthetic construct DNA, clone: pF1KA1604, Homo sapiens KIAA1604 gene for KIAA1604 protein, complete cds, without stop codon, in Flexi system.
BC016651 - Homo sapiens CWC22 spliceosome-associated protein homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4385766), partial cds.
BC031216 - Homo sapiens CWC22 spliceosome-associated protein homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:5269056), partial cds.
AK025635 - Homo sapiens cDNA: FLJ21982 fis, clone HEP06188.
BC057826 - Homo sapiens CWC22 spliceosome-associated protein homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:30334112), partial cds.
JD316474 - Sequence 297498 from Patent EP1572962.

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

Protein Q9HCG8 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: CWC22_HUMAN, KIAA1604, NCM, NM_020943, NP_065994, Q05DC2, Q4G135, Q52LF0, Q6PEX2, Q7Z6I0, Q9H5L3, Q9H6Q6, Q9HCG8
UCSC ID: uc010frh.1
RefSeq Accession: NM_020943
Protein: Q9HCG8 (aka CWC22_HUMAN)
CCDS: CCDS46465.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020943.2
exon count: 20CDS single in 3' UTR: no RNA size: 3279
ORF size: 2727CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5567.00frame shift in genome: no % Coverage: 100.00
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.