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STAG1 STAG1 cohesin complex component [ Homo sapiens (human) ]

Gene ID: 10274, updated on 27-Nov-2024

Summary

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Official Symbol
STAG1provided by HGNC
Official Full Name
STAG1 cohesin complex componentprovided by HGNC
Primary source
HGNC:HGNC:11354
See related
Ensembl:ENSG00000118007 MIM:604358; AllianceGenome:HGNC:11354
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SA1; MRD47; SCC3A
Summary
This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in ovary (RPKM 10.7), endometrium (RPKM 9.9) and 25 other tissues See more
Orthologs
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Genomic context

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See STAG1 in Genome Data Viewer
Location:
3q22.3
Exon count:
39
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (136336236..136752378, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (139076901..139493092, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (136055078..136471220, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:135942902-135943448 Neighboring gene ribosomal protein L31 pseudogene 23 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:135968821-135969687 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:136015730-136016305 Neighboring gene propionyl-CoA carboxylase subunit beta Neighboring gene RNA, U6 small nuclear 1284, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:136344516-136345016 Neighboring gene RNY4 pseudogene 4 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 10 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:136442929-136443555 Neighboring gene RNA, U6 small nuclear 789, pseudogene Neighboring gene hESC enhancers GRCh37_chr3:136470665-136471596 and GRCh37_chr3:136471597-136472528 Neighboring gene DNAJC8 pseudogene 2 Neighboring gene STAG1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20588 Neighboring gene sulfotransferase family 1D member 1 pseudogene 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. Single Nucleotide Polymorphism Facilitated Down-Regulation of the Cohesin Stromal Antigen-1: Implications for Colorectal Cancer Racial Disparities. Datta S, et al. Neoplasia, 2018 Mar. PMID 29471289, Free PMC Article
  2. STAG1 mutations cause a novel cohesinopathy characterised by unspecific syndromic intellectual disability. Lehalle D, et al. J Med Genet, 2017 Jul. PMID 28119487
  3. Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies. Saitta C, et al. Blood Cancer J, 2022 Jun 2. PMID 35654786, Free PMC Article
  4. Whole Exome Sequencing Identifies Cohesin Component STAG1 Mutation in de novo Acute Myeloid Leukemia (FAB M2): A Pilot Study with Cytogenetics, Clinical and Prognostic Implications. Sakthivel KM, et al. J Environ Pathol Toxicol Oncol, 2021. PMID 33639073
  5. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Richart L, et al. Nucleic Acids Res, 2021 Nov 8. PMID 34648034, Free PMC Article

See all (93) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
    Title: Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
  2. Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2.
    Title: Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2.
  3. Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies.
    Title: Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies.
  4. PD-L1 regulates genomic stability via interaction with cohesin-SA1 in the nucleus.
    Title: PD-L1 regulates genomic stability via interaction with cohesin-SA1 in the nucleus.
  5. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells.
    Title: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells.
  6. STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers.
    Title: STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers.
  7. Specialized functions of cohesins STAG1 and STAG2 in 3D genome architecture.
    Title: Specialized functions of cohesins STAG1 and STAG2 in 3D genome architecture.
  8. Whole Exome Sequencing Identifies Cohesin Component STAG1 Mutation in de novo Acute Myeloid Leukemia (FAB M2): A Pilot Study with Cytogenetics, Clinical and Prognostic Implications.
    Title: Whole Exome Sequencing Identifies Cohesin Component STAG1 Mutation in de novo Acute Myeloid Leukemia (FAB M2): A Pilot Study with Cytogenetics, Clinical and Prognostic Implications.
  9. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.
    Title: Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.
  10. Study provides a comprehensive review of the function of STAG1/2 in human physiology and disease and an integrative analysis of available omics data on STAG alterations in a wide array of cancers, comprising 53 691 patients and 1067 cell lines.
    Title: STAG Mutations in Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (26)

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

Associated conditions

Description Tests
Intellectual disability, autosomal dominant 47
MedGen: C4539951 OMIM: 617635 GeneReviews: Not available
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EBI GWAS Catalog

Description
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EBI GWAS Catalog
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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

  • DKFZp781D1416

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in establishment of mitotic sister chromatid cohesion NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mitotic spindle assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in sister chromatid cohesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome TAS
Traceable Author Statement
more info
  
located_in chromosome, centromeric region TAS
Traceable Author Statement
more info
  
part_of cohesin complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of cohesin complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of mitotic cohesin complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in mitotic spindle pole IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
cohesin subunit SA-1
Names
SCC3 homolog 1
nuclear protein stromal antigen 1
sister chromatid cohesion 3 homolog A
stromal antigen 1

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.

mRNA and Protein(s)

  1. NM_005862.3 → NP_005853.2  cohesin subunit SA-1

    See identical proteins and their annotated locations for NP_005853.2

    Status: REVIEWED

    Source sequence(s)
    AC069524, BC017735, BC064699
    Consensus CDS
    CCDS3090.1
    UniProtKB/Swiss-Prot
    O00539, Q6P275, Q8WVM7
    UniProtKB/TrEMBL
    Q4LE48
    Related
    ENSP00000372689.2, ENST00000383202.7
    Conserved Domains (2) summary
    pfam08514
    Location:160 → 268
    STAG; STAG domain
    pfam14621
    Location:3 → 83
    RFX5_DNA_bdg; RFX5 DNA-binding domain

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    136336236..136752378 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047447229.1 → XP_047303185.1  cohesin subunit SA-1 isoform X1

    Related
    ENSP00000404396.2, ENST00000434713.6

  2. XM_047447228.1 → XP_047303184.1  cohesin subunit SA-1 isoform X1

  3. XM_047447231.1 → XP_047303187.1  cohesin subunit SA-1 isoform X2

  4. XM_047447230.1 → XP_047303186.1  cohesin subunit SA-1 isoform X2

  5. XM_047447235.1 → XP_047303191.1  cohesin subunit SA-1 isoform X3

  6. XM_017005525.2 → XP_016861014.1  cohesin subunit SA-1 isoform X4

    UniProtKB/TrEMBL
    B4E2Q7

RNA

  1. XR_001739978.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    139076901..139493092 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344912.1 → XP_054200887.1  cohesin subunit SA-1 isoform X1

  2. XM_054344911.1 → XP_054200886.1  cohesin subunit SA-1 isoform X1

  3. XM_054344914.1 → XP_054200889.1  cohesin subunit SA-1 isoform X2

  4. XM_054344913.1 → XP_054200888.1  cohesin subunit SA-1 isoform X2

  5. XM_054344915.1 → XP_054200890.1  cohesin subunit SA-1 isoform X3

  6. XM_054344916.1 → XP_054200891.1  cohesin subunit SA-1 isoform X4

RNA

  1. XR_008486626.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WVM7.3 GenPept UniProtKB/Swiss-Prot:Q8WVM7

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