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Aliases for SCNM1 Gene

Aliases for SCNM1 Gene

  • Sodium Channel Modifier 1 2 3 5

External Ids for SCNM1 Gene

Previous GeneCards Identifiers for SCNM1 Gene

  • GC01P147913
  • GC01P148355
  • GC01P147951
  • GC01P149405

Summaries for SCNM1 Gene

Entrez Gene Summary for SCNM1 Gene

  • SCNM1 is a zinc finger protein and putative splicing factor. In mice, Scnm1 modifies phenotypic expression of Scn8a (MIM 600702) mutations (Buchner et al., 2003 [PubMed 12920299]).[supplied by OMIM, Oct 2009]

GeneCards Summary for SCNM1 Gene

SCNM1 (Sodium Channel Modifier 1) is a Protein Coding gene. Diseases associated with SCNM1 include Lennox-Gastaut Syndrome. GO annotations related to this gene include enzyme binding.

UniProtKB/Swiss-Prot for SCNM1 Gene

  • Plays a role in RNA splicing, possibly contributing to the recognition of non-consensus donor sites.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCNM1 Gene

Genomics for SCNM1 Gene

Regulatory Elements for SCNM1 Gene

Enhancers for SCNM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F151193 1 FANTOM5 ENCODE 22.5 +41.0 40983 7.7 PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 SETDB1 GOLPH3L PRPF3 GABPB2 UBE2D3P3 MRPL9 RPS10P6 SCNM1 LYSMD1 RN7SL444P
GH01F151068 0.8 ENCODE 11.7 -86.2 -86179 3.3 HDGF PKNOX1 ARNT CREB3L1 SIN3A FEZF1 ZNF2 YY1 ZNF416 ZNF143 GABPB2 MRPL9 SETDB1 PRPF3 UBE2D3P3 LYSMD1 CTSK GOLPH3L BNIPL RPS10P6
GH01F151004 0.4 ENCODE 11.7 -149.2 -149220 5.2 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC SETDB1 GOLPH3L MRPL9 GABPB2 PRPF3 UBE2D3P3 LYSMD1 CTSK C1orf56 HORMAD1
GH01F151345 1.1 ENCODE 11.6 +190.4 190421 2.9 PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A YBX1 DMAP1 ZNF2 YY1 ZNF143 SETDB1 GOLPH3L UBE2D3P3 RPS10P6 CTSK GABPB2 SCNM1 ENSG00000229021 RN7SL444P GBAT2
GH01F150874 0.2 ENCODE 11.6 -280.8 -280764 3.7 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 HORMAD1 SETDB1 GOLPH3L CYCSP51 PRPF3 SF3B4 ARNT UBE2D3P3 MRPL9 RPS10P6
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SCNM1 on UCSC Golden Path with GeneCards custom track

Promoters for SCNM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000544857 836 1801 MAZ ETV1 CBFB CHD1 ZMYM3 MAX ZNF366 POLR2A TARDBP EED

Genomic Location for SCNM1 Gene

Chromosome:
1
Start:
151,156,664 bp from pter
End:
151,170,297 bp from pter
Size:
13,634 bases
Orientation:
Plus strand

Genomic View for SCNM1 Gene

Genes around SCNM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCNM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCNM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCNM1 Gene

Proteins for SCNM1 Gene

  • Protein details for SCNM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BWG6-SCNM1_HUMAN
    Recommended name:
    Sodium channel modifier 1
    Protein Accession:
    Q9BWG6
    Secondary Accessions:
    • B4DWR1
    • Q5JR74

    Protein attributes for SCNM1 Gene

    Size:
    230 amino acids
    Molecular mass:
    25949 Da
    Quaternary structure:
    • Interacts with LUC7L2 and SNRNP70, which suggests a role as a spliceosome component.

    Alternative splice isoforms for SCNM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCNM1 Gene

Post-translational modifications for SCNM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SCNM1 Gene

Antibody Products

  • Abcam antibodies for SCNM1

No data available for DME Specific Peptides for SCNM1 Gene

Domains & Families for SCNM1 Gene

Protein Domains for SCNM1 Gene

Suggested Antigen Peptide Sequences for SCNM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BWG6

UniProtKB/Swiss-Prot:

SCNM1_HUMAN :
  • Contains 1 matrin-type zinc finger.
Similarity:
  • Contains 1 matrin-type zinc finger.
genes like me logo Genes that share domains with SCNM1: view

No data available for Gene Families for SCNM1 Gene

Function for SCNM1 Gene

Molecular function for SCNM1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in RNA splicing, possibly contributing to the recognition of non-consensus donor sites.

Gene Ontology (GO) - Molecular Function for SCNM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0019899 enzyme binding IPI 23382074
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SCNM1: view
genes like me logo Genes that share phenotypes with SCNM1: view

Animal Models for SCNM1 Gene

MGI Knock Outs for SCNM1:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCNM1 Gene

Localization for SCNM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCNM1 Gene

Nucleus. Nucleus speckle. Note=Colocalizes with LUC7L2 and SNRNP70 in nuclear speckles. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SCNM1 Gene COMPARTMENTS Subcellular localization image for SCNM1 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SCNM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA --
GO:0016607 nuclear speck IEA --
genes like me logo Genes that share ontologies with SCNM1: view

Pathways & Interactions for SCNM1 Gene

SuperPathways for SCNM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCNM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SCNM1: view

No data available for Pathways by source and SIGNOR curated interactions for SCNM1 Gene

Transcripts for SCNM1 Gene

Unigene Clusters for SCNM1 Gene

Sodium channel modifier 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCNM1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b · 7c
SP1: - - - - -
SP2: - - - - -
SP3: - - - -
SP4: - - -
SP5: - -
SP6: - -
SP7: -

Relevant External Links for SCNM1 Gene

GeneLoc Exon Structure for
SCNM1
ECgene alternative splicing isoforms for
SCNM1

Expression for SCNM1 Gene

mRNA expression in normal human tissues for SCNM1 Gene

mRNA differential expression in normal tissues according to GTEx for SCNM1 Gene

This gene is overexpressed in Whole Blood (x4.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SCNM1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SCNM1 Gene:

SCNM1

SOURCE GeneReport for Unigene cluster for SCNM1 Gene:

Hs.732060
genes like me logo Genes that share expression patterns with SCNM1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SCNM1 Gene

Orthologs for SCNM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCNM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCNM1 34 35
  • 99.57 (n)
cow
(Bos Taurus)
Mammalia SCNM1 34 35
  • 90.87 (n)
dog
(Canis familiaris)
Mammalia SCNM1 34 35
  • 88.41 (n)
mouse
(Mus musculus)
Mammalia Scnm1 34 16 35
  • 84.59 (n)
rat
(Rattus norvegicus)
Mammalia Scnm1 34
  • 84.43 (n)
oppossum
(Monodelphis domestica)
Mammalia SCNM1 35
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCNM1 34 35
  • 55.31 (n)
lizard
(Anolis carolinensis)
Reptilia SCNM1 35
  • 47 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scnm1 34
  • 57.74 (n)
zebrafish
(Danio rerio)
Actinopterygii scnm1 34 35
  • 51.77 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 29 (a)
OneToOne
Species where no ortholog for SCNM1 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCNM1 Gene

ENSEMBL:
Gene Tree for SCNM1 (if available)
TreeFam:
Gene Tree for SCNM1 (if available)

Paralogs for SCNM1 Gene

No data available for Paralogs for SCNM1 Gene

Variants for SCNM1 Gene

Sequence variations from dbSNP and Humsavar for SCNM1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1115 -- 151,168,256(-) CTCCT(C/T)GGCCT nc-transcript-variant, reference, missense
rs111733362 -- 151,168,601(+) CGGGG(G/T)TTCTC intron-variant
rs111868471 -- 151,167,608(+) GGGTG(C/G)ATCAC intron-variant, upstream-variant-2KB
rs113051510 -- 151,165,032(+) AGGAC(C/T)AAATC intron-variant, upstream-variant-2KB
rs113054372 -- 151,167,568(+) GACTC(A/G)CGCCT intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SCNM1 Gene

Variant ID Type Subtype PubMed ID
dgv2n68 CNV loss 17160897
esv3587520 CNV loss 21293372
nsv522840 CNV gain 19592680

Variation tolerance for SCNM1 Gene

Residual Variation Intolerance Score: 61.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.86; 48.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCNM1 Gene

Human Gene Mutation Database (HGMD)
SCNM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCNM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCNM1 Gene

Disorders for SCNM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCNM1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
lennox-gastaut syndrome
  • lennox syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SCNM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SCNM1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SCNM1
genes like me logo Genes that share disorders with SCNM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCNM1 Gene

Publications for SCNM1 Gene

  1. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. (PMID: 12920299) Buchner D.A. … Meisler M.H. (Science 2003) 2 3 22 64
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. (PMID: 27107012) Yachie N. … Roth F.P. (Mol. Syst. Biol. 2016) 3 64

Products for SCNM1 Gene

Sources for SCNM1 Gene

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