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Aliases for SNAPC4 Gene

Aliases for SNAPC4 Gene

  • Small Nuclear RNA Activating Complex Polypeptide 4 2 3 5
  • Proximal Sequence Element-Binding Transcription Factor Subunit Alpha 3 4
  • SnRNA-Activating Protein Complex 190 KDa Subunit 3 4
  • PSE-Binding Factor Subunit Alpha 3 4
  • SNAPc 190 KDa Subunit 3 4
  • PTF Subunit Alpha 3 4
  • SNAPc Subunit 4 3 4
  • SNAP190 3 4
  • Small Nuclear RNA Activating Complex, Polypeptide 4, 190kDa 2
  • Small Nuclear RNA Activating Complex, Polypeptide 4, 190kD 2
  • SnRNA-Activating Protein Complex Subunit 4 3
  • PTFalpha 3

External Ids for SNAPC4 Gene

Previous GeneCards Identifiers for SNAPC4 Gene

  • GC09M130337
  • GC09M130959
  • GC09M132711
  • GC09M134627
  • GC09M136545
  • GC09M138389
  • GC09M139270
  • GC09M108729

Summaries for SNAPC4 Gene

Entrez Gene Summary for SNAPC4 Gene

  • This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]

GeneCards Summary for SNAPC4 Gene

SNAPC4 (Small Nuclear RNA Activating Complex Polypeptide 4) is a Protein Coding gene. Diseases associated with SNAPC4 include Spondylitis. Among its related pathways are RNA Polymerase III Transcription Initiation and Formation of HIV-1 elongation complex containing HIV-1 Tat. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is MYB.

UniProtKB/Swiss-Prot for SNAPC4 Gene

  • 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.

Gene Wiki entry for SNAPC4 Gene

Additional gene information for SNAPC4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNAPC4 Gene

Genomics for SNAPC4 Gene

GeneHancer (GH) Regulatory Elements for SNAPC4 Gene

Promoters and enhancers for SNAPC4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J136398 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 672.1 +0.4 387 3 HDGF ARID4B SIN3A ZNF766 ZNF207 ZNF143 DEK REST ZNF592 KAT8 SNAPC4 INPP5E DNLZ ENTR1 ANAPC2 CARD9 SEC16A FAM69B TRAF2
GH09J136358 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 27.9 +38.6 38607 5.5 HDGF SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B DNLZ RABL6 INPP5E ANAPC2 MAN1B1 SNAPC4 SNHG7 NPDC1 ENTR1 CARD9
GH09J136481 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 25.1 -83.5 -83470 4.6 HDGF PKNOX1 CLOCK SMAD1 FOXA2 ZFP64 ARID4B SIN3A DMAP1 ZNF2 SEC16A C9orf163 INPP5E SNAPC4 ANAPC2 SNHG7 ENTR1 MAN1B1 NDOR1 EXD3
GH09J136408 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.8 -10.2 -10245 3.6 HDGF CLOCK SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ENTR1 PIR36061 PIR60193 PMPCA GC09M136410 INPP5E DNLZ SEC16A SNAPC4 SNHG7
GH09J136684 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 19.1 -286.9 -286946 4.7 SIN3A IRF4 YY1 POLR2B ZNF207 ZNF143 JUNB REST SMARCB1 ZNF592 AGPAT2 DPH7 INPP5E ANAPC2 EXD3 SNAPC4 MAN1B1 ARRDC1-AS1 EHMT1 QSOX2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SNAPC4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SNAPC4 gene promoter:
  • p53
  • c-Myb
  • Lmo2
  • SEF-1 (1)
  • Pax-6
  • Olf-1
  • Pbx1a
  • NRF-2

Genomic Locations for SNAPC4 Gene

Genomic Locations for SNAPC4 Gene
chr9:136,375,571-136,400,208
(GRCh38/hg38)
Size:
24,638 bases
Orientation:
Minus strand
chr9:139,270,029-139,293,249
(GRCh37/hg19)
Size:
23,221 bases
Orientation:
Minus strand

Genomic View for SNAPC4 Gene

Genes around SNAPC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNAPC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNAPC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNAPC4 Gene

Proteins for SNAPC4 Gene

  • Protein details for SNAPC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5SXM2-SNPC4_HUMAN
    Recommended name:
    snRNA-activating protein complex subunit 4
    Protein Accession:
    Q5SXM2
    Secondary Accessions:
    • Q9Y6P7

    Protein attributes for SNAPC4 Gene

    Size:
    1469 amino acids
    Molecular mass:
    159433 Da
    Quaternary structure:
    • Part of the SNAPc complex composed of 5 subunits: SNAPC1, SNAPC2, SNAPC3, SNAPC4 and SNAPC5. SNAPC4 interacts with SNAPC1, SNAPC2, SNAPC5, BRF2 and TBP.

neXtProt entry for SNAPC4 Gene

Post-translational modifications for SNAPC4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SNAPC4 Gene

No data available for DME Specific Peptides for SNAPC4 Gene

Domains & Families for SNAPC4 Gene

Gene Families for SNAPC4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SNAPC4 Gene

Suggested Antigen Peptide Sequences for SNAPC4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SNAPC4: view

No data available for UniProtKB/Swiss-Prot for SNAPC4 Gene

Function for SNAPC4 Gene

Molecular function for SNAPC4 Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for SNAPC4 Gene

Gene Ontology (GO) - Molecular Function for SNAPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001135 transcription factor activity, RNA polymerase II transcription factor recruiting IBA --
GO:0003677 DNA binding IDA,IEA 11056176
GO:0003700 DNA binding transcription factor activity TAS 9418884
GO:0043565 sequence-specific DNA binding IBA --
genes like me logo Genes that share ontologies with SNAPC4: view
genes like me logo Genes that share phenotypes with SNAPC4: view

Animal Models for SNAPC4 Gene

MGI Knock Outs for SNAPC4:
  • Snapc4 Snapc4<tm1a(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for SNAPC4 Gene

miRTarBase miRNAs that target SNAPC4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNAPC4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SNAPC4 Gene

Localization for SNAPC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNAPC4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SNAPC4 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SNAPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IC,TAS 11056176
GO:0005654 nucleoplasm TAS --
GO:0019185 snRNA-activating protein complex IDA,IEA 9418884
genes like me logo Genes that share ontologies with SNAPC4: view

Pathways & Interactions for SNAPC4 Gene

genes like me logo Genes that share pathways with SNAPC4: view

Gene Ontology (GO) - Biological Process for SNAPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA --
GO:0006366 transcription by RNA polymerase II TAS 9418884
GO:0006383 transcription by RNA polymerase III TAS 9418884
genes like me logo Genes that share ontologies with SNAPC4: view

No data available for SIGNOR curated interactions for SNAPC4 Gene

Drugs & Compounds for SNAPC4 Gene

No Compound Related Data Available

Transcripts for SNAPC4 Gene

mRNA/cDNA for SNAPC4 Gene

Unigene Clusters for SNAPC4 Gene

Small nuclear RNA activating complex, polypeptide 4, 190kDa:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNAPC4

Alternative Splicing Database (ASD) splice patterns (SP) for SNAPC4 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^
SP1:
SP2: -
SP3: -
SP4: -
SP5: -
SP6:
SP7:
SP8:
SP9: -
SP10:

ExUns: 19 ^ 20 ^ 21 ^ 22 ^ 23
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for SNAPC4 Gene

GeneLoc Exon Structure for
SNAPC4
ECgene alternative splicing isoforms for
SNAPC4

Expression for SNAPC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNAPC4 Gene

Protein differential expression in normal tissues from HIPED for SNAPC4 Gene

This gene is overexpressed in Pancreatic juice (31.2) and Lung (28.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SNAPC4 Gene



NURSA nuclear receptor signaling pathways regulating expression of SNAPC4 Gene:

SNAPC4

SOURCE GeneReport for Unigene cluster for SNAPC4 Gene:

Hs.113265
genes like me logo Genes that share expression patterns with SNAPC4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNAPC4 Gene

Orthologs for SNAPC4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SNAPC4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SNAPC4 34 33
  • 96.79 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SNAPC4 34 33
  • 76.31 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Snapc4 33
  • 73.26 (n)
mouse
(Mus musculus)
Mammalia Snapc4 16 34 33
  • 72.85 (n)
cow
(Bos Taurus)
Mammalia SNAPC4 34 33
  • 70.92 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SNAPC4 34
  • 52 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SNAPC4 34
  • 45 (a)
OneToOne
chicken
(Gallus gallus)
Aves SNAPC4 34 33
  • 54.13 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SNAPC4 34
  • 66 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii snapc4 34
  • 40 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Pbp95 34
  • 22 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea gei-11 35
  • 29 (a)
snpc-4 34
  • 22 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BAS1 36 34
  • 15 (a)
Species where no ortholog for SNAPC4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SNAPC4 Gene

ENSEMBL:
Gene Tree for SNAPC4 (if available)
TreeFam:
Gene Tree for SNAPC4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SNAPC4: view image

Paralogs for SNAPC4 Gene

Paralogs for SNAPC4 Gene

Pseudogenes.org Pseudogenes for SNAPC4 Gene

genes like me logo Genes that share paralogs with SNAPC4: view

Variants for SNAPC4 Gene

Sequence variations from dbSNP and Humsavar for SNAPC4 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs771245174 likely-benign, Long QT syndrome 136,377,892(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs10781507 benign, not specified 136,377,606(-) A/G coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs3812565 benign, not specified 136,378,050(-) T/C coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs1000074094 -- 136,396,543(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000346182 -- 136,399,512(-) C/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SNAPC4 Gene

Variant ID Type Subtype PubMed ID
esv2759720 CNV loss 17122850
nsv1046074 CNV gain 25217958
nsv469918 CNV loss 18288195
nsv509333 CNV insertion 20534489
nsv615963 CNV loss 21841781
nsv6764 CNV deletion 18451855
nsv825173 CNV gain 20364138
nsv831760 CNV loss 17160897
nsv951202 CNV deletion 24416366

Variation tolerance for SNAPC4 Gene

Residual Variation Intolerance Score: 98.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.15; 95.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SNAPC4 Gene

Human Gene Mutation Database (HGMD)
SNAPC4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNAPC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNAPC4 Gene

Disorders for SNAPC4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SNAPC4 Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
spondylitis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SNAPC4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SNAPC4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SNAPC4 Gene

Publications for SNAPC4 Gene

  1. The large subunit of basal transcription factor SNAPc is a Myb domain protein that interacts with Oct-1. (PMID: 9418884) Wong MW … Hernandez N (Molecular and cellular biology 1998) 2 3 4 22 58
  2. The small nuclear RNA-activating protein 190 Myb DNA binding domain stimulates TATA box-binding protein-TATA box recognition. (PMID: 12621023) Hinkley CS … Henry RW (The Journal of biological chemistry 2003) 3 4 22 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. The protein kinase CK2 phosphorylates SNAP190 to negatively regulate SNAPC DNA binding and human U6 transcription by RNA polymerase III. (PMID: 17670747) Gu L … Henry RW (The Journal of biological chemistry 2007) 3 22 58
  5. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4 58

Products for SNAPC4 Gene

Sources for SNAPC4 Gene

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