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    SBNO1 strawberry notch homolog 1 [ Homo sapiens (human) ]

    Gene ID: 55206, updated on 5-May-2024

    Summary

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    Official Symbol
    SBNO1provided by HGNC
    Official Full Name
    strawberry notch homolog 1provided by HGNC
    Primary source
    HGNC:HGNC:22973
    See related
    Ensembl:ENSG00000139697 MIM:614274; AllianceGenome:HGNC:22973
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Sno; MOP3
    Summary
    Predicted to enable chromatin DNA binding activity and histone binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 27.6), thyroid (RPKM 6.9) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q24.31
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123289109..123364847, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123285663..123361354, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (123773656..123849394, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123749585-123749777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5032 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123754459-123755207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5033 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:123756263-123756770 Neighboring gene cyclin dependent kinase 2 associated protein 1 Neighboring gene RNA, 5S ribosomal pseudogene 375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5036 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123825715-123825938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:123848060-123848778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7260 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123855180-123855353 Neighboring gene SBNO1 antisense RNA 1 Neighboring gene microRNA 8072 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123867650-123867872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123867837-123868567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5043 Neighboring gene lysine methyltransferase 5A Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123886419-123887182 Neighboring gene Rab interacting lysosomal protein like 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Genomic structural variants are linked with intellectual disability. Bulayeva K, et al. J Neural Transm (Vienna), 2015 Sep. PMID 25626716, Free PMC Article
    2. Study of Strawberry Notch homolog 1 and 2 expression in human glioblastoma. Coppieters N, et al. J Neurooncol, 2023 Feb. PMID 36695974
    3. Notch signaling pathway and Cdx2 expression in the development of Barrett's esophagus. Tamagawa Y, et al. Lab Invest, 2012 Jun. PMID 22449796
    4. Common variants at 12q15 and 12q24 are associated with infant head circumference. Taal HR, et al. Nat Genet, 2012 Apr 15. PMID 22504419, Free PMC Article
    5. Identification of Myc-associated protein with JmjC domain as a novel therapeutic target oncogene for lung cancer. Suzuki C, et al. Mol Cancer Ther, 2007 Feb. PMID 17308053

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study of Strawberry Notch homolog 1 and 2 expression in human glioblastoma.
      Title: Study of Strawberry Notch homolog 1 and 2 expression in human glioblastoma.
    2. Enhanced expression of Cdx2 by stimulation with bile acids may induce intestinal differentiation of esophageal columnar cells by interaction with the Notch signaling pathway.
      Title: Notch signaling pathway and Cdx2 expression in the development of Barrett's esophagus.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Common variants at 12q15 and 12q24 are associated with infant head circumference.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10701, FLJ10833, FLJ14066, FLJ16176, FLJ35199

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein strawberry notch homolog 1
    Names
    monocyte protein 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_052874.1 RefSeqGene

      Range
      5363..81101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001167856.3 → NP_001161328.1  protein strawberry notch homolog 1 isoform 1

      See identical proteins and their annotated locations for NP_001161328.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC068768, AC137767
      Consensus CDS
      CCDS53844.1
      UniProtKB/Swiss-Prot
      A3KN83, Q05C06, Q3ZTS3, Q9H3T8, Q9NVB2
      Related
      ENSP00000473665.1, ENST00000602398.3
      Conserved Domains (3) summary
      pfam09595
      Location:26 → 151
      Metaviral_G; Metaviral_G glycoprotein
      pfam13871
      Location:872 → 1148
      Helicase_C_4; C-terminal domain on Strawberry notch homologue
      pfam13872
      Location:258 → 560
      AAA_34; P-loop containing NTP hydrolase pore-1

    2. NM_018183.5 → NP_060653.3  protein strawberry notch homolog 1 isoform 2

      See identical proteins and their annotated locations for NP_060653.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC068768, AC137767
      Consensus CDS
      CCDS9246.1
      UniProtKB/Swiss-Prot
      A3KN83
      Related
      ENSP00000267176.4, ENST00000267176.8
      Conserved Domains (3) summary
      pfam09595
      Location:26 → 150
      Metaviral_G; Metaviral_G glycoprotein
      pfam13871
      Location:871 → 1147
      Helicase_C_4; C-terminal domain on Strawberry notch homologue
      pfam13872
      Location:257 → 559
      AAA_34; P-loop containing NTP hydrolase pore-1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      123289109..123364847 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      123285663..123361354 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A3KN83.1 GenPept UniProtKB/Swiss-Prot:A3KN83

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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