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

Gene ID: 55206, updated on 27-Nov-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 DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
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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See SBNO1 in Genome Data Viewer
Location:
12q24.31
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123289109..123364847, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123285663..123361354, complement)
RS_2024_09 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 (56) 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)

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
  
Process Evidence Code Pubs
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
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_2024_08

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.

Chemical Information
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