Human Gene CCDC49 (uc002hqu.1)
  Description: coiled-coil domain containing 49
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: hg18 chr17:34,210,972-34,235,115 Size: 24,144 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg18 chr17:34,211,871-34,234,962 Size: 23,092 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:34,210,972-34,235,115)mRNA (may differ from genome)Protein (425 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDMGIPubMedReactomeTreefam
UniProtKBBioGrid CRISPR DB

-  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.

-  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


-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -40.60153-0.265 Picture PostScript Text
3' UTR -252.10899-0.280 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

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 BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  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.
AK302983 - Homo sapiens cDNA FLJ55385 complete cds.
BC003085 - Homo sapiens coiled-coil domain containing 49, mRNA (cDNA clone IMAGE:3358029), partial cds.
JD362142 - Sequence 343166 from Patent EP1572962.
JD424496 - Sequence 405520 from Patent EP1572962.
JD530001 - Sequence 511025 from Patent EP1572962.
JD494832 - Sequence 475856 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.
JD083117 - Sequence 64141 from Patent EP1572962.
JD044078 - Sequence 25102 from Patent EP1572962.
JD235353 - Sequence 216377 from Patent EP1572962.
JD174369 - Sequence 155393 from Patent EP1572962.
JD265332 - Sequence 246356 from Patent EP1572962.
JD225176 - Sequence 206200 from Patent EP1572962.
JD263477 - Sequence 244501 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, CCD49_HUMAN, NM_017748, NP_060218, Q68DK5, Q9NXE8
UCSC ID: uc002hqu.1
RefSeq Accession: NM_017748
Protein: Q9NXE8 (aka CWC25_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017748.3
exon count: 10CDS single in 3' UTR: no RNA size: 2347
ORF size: 1278CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2653.00frame shift in genome: no % Coverage: 99.28
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.