Human Gene SNAPC5 (uc002apu.1) Description and Page Index
  Description: Homo sapiens small nuclear RNA activating complex, polypeptide 5, 19kDa (SNAPC5), mRNA.
RefSeq Summary (NM_006049): This gene encodes a subunit of the small nuclear RNA (snRNA)-activating protein complex that plays a role in the transcription of snRNA genes. This complex binds to the promoters of snRNA genes transcribed by either RNA polymerase II or III and recruits other regulatory factors to activate snRNA gene transcription. The encoded protein may play a role in stabilizing this complex. A pseudogene of this gene has been identified on chromosome 6. [provided by RefSeq, Jul 2016].
Transcript (Including UTRs)
   Position: hg19 chr15:66,782,666-66,790,146 Size: 7,481 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr15:66,786,774-66,790,069 Size: 3,296 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:66,782,666-66,790,146)mRNA (may differ from genome)Protein (98 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SNPC5_HUMAN
DESCRIPTION: RecName: Full=snRNA-activating protein complex subunit 5; Short=SNAPc subunit 5; AltName: Full=Small nuclear RNA-activating complex polypeptide 5; AltName: Full=snRNA-activating protein complex 19 kDa subunit; Short=SNAPc 19 kDa subunit;
FUNCTION: Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box.
SUBUNIT: Part of the SNAPc complex composed of 5 subunits: SNAPC1, SNAPC2, SNAPC3, SNAPC4 and SNAPC5. SNAPC5 interacts with SNAPC4.
SUBCELLULAR LOCATION: Nucleus.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SNAPC5
CDC HuGE Published Literature: SNAPC5
Positive Disease Associations: Macular Degeneration
Related Studies:
  1. Macular Degeneration
    , , . [PubMed 0]

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.73 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 472.06 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 -27.2077-0.353 Picture PostScript Text
3' UTR -143.80411-0.350 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
  Pfam Domains:
PF15497 - snRNA-activating protein complex subunit 19, SNAPc subunit 19

ModBase Predicted Comparative 3D Structure on O75971
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006384 transcription initiation from RNA polymerase III promoter
GO:0042795 snRNA transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  BC066984 - Homo sapiens cDNA clone IMAGE:4826623.
LF384557 - JP 2014500723-A/192060: Polycomb-Associated Non-Coding RNAs.
AK024763 - Homo sapiens cDNA: FLJ21110 fis, clone CAS05377.
AK292051 - Homo sapiens cDNA FLJ76570 complete cds, highly similar to Homo sapiens small nuclear RNA activating complex, polypeptide 5, 19kDa, mRNA.
BC014315 - Homo sapiens small nuclear RNA activating complex, polypeptide 5, 19kDa, mRNA (cDNA clone MGC:22700 IMAGE:3997264), complete cds.
AF093593 - Homo sapiens snRNA activating protein complex 19kDa subunit (SNAP19) mRNA, complete cds.
AK312018 - Homo sapiens cDNA, FLJ92293.
KJ904649 - Synthetic construct Homo sapiens clone ccsbBroadEn_14043 SNAPC5 gene, encodes complete protein.
AB464224 - Synthetic construct DNA, clone: pF1KB7505, Homo sapiens SNAPC5 gene for small nuclear RNA activating complex, polypeptide 5, 19kDa, without stop codon, in Flexi system.
LF377480 - JP 2014500723-A/184983: Polycomb-Associated Non-Coding RNAs.
MA620134 - JP 2018138019-A/192060: Polycomb-Associated Non-Coding RNAs.
MA613057 - JP 2018138019-A/184983: Polycomb-Associated Non-Coding RNAs.

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

Protein O75971 (Reactome details) participates in the following event(s):

R-HSA-83791 Binding of SNAPc, Oct-1, and Staf to Type 3 Promoter
R-HSA-6810239 SNAPc binds PSE of snRNA gene (U1, U2, U4, U4atac, U5, U11, U12)
R-HSA-83793 Binding of TFIIIB to SNAPc:Oct-1:Staf:Type 3 Promoter Complex
R-HSA-112054 RNA Polymerase III Abortive Initiation At Type 3 Open Promoters
R-HSA-112156 RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters
R-HSA-112152 RNA Polymerase III Promoter Opening at Type 3 Promoters
R-HSA-6810234 General transcription factors bind SNAPc:POU2F1:ZNF143:snRNA gene
R-HSA-83803 Recruitment of RNA Polymerase III to TFIIIB:SNAPc:Type 3 Promoter Complex
R-HSA-6810233 CDK7 phosphorylates serine-5 and serine-7 of heptad repeats in C-terminal domain of RNA polymerase II at snRNA promoter
R-HSA-6810238 RNA polymerase II binds initiation factors at promoter of snRNA gene (U1, U2, U4, U4atac, U5, U11, U12)
R-HSA-6810235 RPAP2 binds RNA polymerase II phosphorylated at serine-7 residues of heptad repeats in the C-terminal domain
R-HSA-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA
R-HSA-76071 RNA Polymerase III Transcription Initiation From Type 3 Promoter
R-HSA-6807505 RNA polymerase II transcribes snRNA genes
R-HSA-749476 RNA Polymerase III Abortive And Retractive Initiation
R-HSA-76046 RNA Polymerase III Transcription Initiation
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74158 RNA Polymerase III Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8K7N6, NM_006049, NP_006040, O75971, Q96CF3, SNAP19, SNPC5_HUMAN
UCSC ID: uc002apu.1
RefSeq Accession: NM_006049
Protein: O75971 (aka SNPC5_HUMAN)
CCDS: CCDS10217.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006049.2
exon count: 4CDS single in 3' UTR: no RNA size: 785
ORF size: 297CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 740.00frame 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.