Human Gene CWC25 (uc002hqu.4) Description and Page Index
  Description: Homo sapiens CWC25 spliceosome-associated protein homolog (S. cerevisiae) (CWC25), transcript variant 1, mRNA.
RefSeq Summary (NM_017748): This gene encodes a factor that is part of the multi-protein C complex involved in pre-mRNA splicing. Alternatively spliced transcripts have been described for this gene. [provided by RefSeq, Nov 2012].
Transcript (Including UTRs)
   Position: hg19 chr17:36,956,687-36,981,603 Size: 24,917 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr17:36,958,345-36,981,436 Size: 23,092 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:36,956,687-36,981,603)mRNA (may differ from genome)Protein (425 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CWC25_HUMAN
DESCRIPTION: RecName: Full=Pre-mRNA-splicing factor CWC25 homolog; AltName: Full=Coiled-coil domain-containing protein 49; AltName: Full=Spliceosome-associated protein homolog CWC25;
SIMILARITY: Belongs to the CWC25 family.

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

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -47.30167-0.283 Picture PostScript Text
3' UTR -488.101658-0.294 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
IPR019339 - CIR_N_dom
IPR022209 - CWC25

Pfam Domains:
PF10197 - N-terminal domain of CBF1 interacting co-repressor CIR
PF12542 - Pre-mRNA splicing factor

ModBase Predicted Comparative 3D Structure on Q9NXE8
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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 orthologGenome Browser
Gene Details  Gene Details Gene Details
Gene Sorter  Gene Sorter Gene Sorter
  EnsemblFlyBase SGD
  Protein SequenceProtein Sequence Protein Sequence
  AlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0000398 mRNA splicing, via spliceosome

Cellular Component:
GO:0005654 nucleoplasm
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  CR749362 - Homo sapiens mRNA; cDNA DKFZp779M0968 (from clone DKFZp779M0968).
AK225373 - Homo sapiens mRNA for hypothetical protein LOC54883 variant, clone: HRC01426.
BC008833 - Homo sapiens coiled-coil domain containing 49, mRNA (cDNA clone MGC:12612 IMAGE:4304656), complete cds.
AK000298 - Homo sapiens cDNA FLJ20291 fis, clone HEP04788.
AK296115 - Homo sapiens cDNA FLJ52308 complete cds.
AB587360 - Synthetic construct DNA, clone: pF1KB0960, Homo sapiens CCDC49 gene for coiled-coil domain containing 49, without stop codon, in Flexi system.
AK316077 - Homo sapiens cDNA, FLJ78976 complete cds.
JD424496 - Sequence 405520 from Patent EP1572962.
JD091646 - Sequence 72670 from Patent EP1572962.
JD244818 - Sequence 225842 from Patent EP1572962.
JD302635 - Sequence 283659 from Patent EP1572962.
JD196221 - Sequence 177245 from Patent EP1572962.
JD530001 - Sequence 511025 from Patent EP1572962.
JD083117 - Sequence 64141 from Patent EP1572962.
JD362142 - Sequence 343166 from Patent EP1572962.
JD044078 - Sequence 25102 from Patent EP1572962.
DQ578103 - Homo sapiens piRNA piR-46215, complete sequence.
JD235353 - Sequence 216377 from Patent EP1572962.
JD174369 - Sequence 155393 from Patent EP1572962.
JD265332 - Sequence 246356 from Patent EP1572962.
AK302983 - Homo sapiens cDNA FLJ55385 complete cds.
BC003085 - Homo sapiens coiled-coil domain containing 49, mRNA (cDNA clone IMAGE:3358029), partial cds.
JD225176 - Sequence 206200 from Patent EP1572962.
JD263477 - Sequence 244501 from Patent EP1572962.
JD494832 - Sequence 475856 from Patent EP1572962.
JD141328 - Sequence 122352 from Patent EP1572962.

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

Protein Q9NXE8 (Reactome details) participates in the following event(s):

R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) 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: A0JLM3, CCDC49, CWC25_HUMAN, NM_017748, NP_060218, Q68DK5, Q9NXE8, uc002hqu.3
UCSC ID: uc002hqu.4
RefSeq Accession: NM_017748
Protein: Q9NXE8 (aka CWC25_HUMAN)
CCDS: CCDS45663.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017748.4
exon count: 10CDS single in 3' UTR: no RNA size: 3112
ORF size: 1278CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2544.00frame shift in genome: no % Coverage: 99.71
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
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-  Methods, Credits, and Use Restrictions
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