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STAG3 STAG3 cohesin complex component [ Homo sapiens (human) ]

Gene ID: 10734, updated on 7-Apr-2024

Summary

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Official Symbol
STAG3provided by HGNC
Official Full Name
STAG3 cohesin complex componentprovided by HGNC
Primary source
HGNC:HGNC:11356
See related
Ensembl:ENSG00000066923 MIM:608489; AllianceGenome:HGNC:11356
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
SA3; SPGF61
Summary
The protein encoded by this gene is expressed in the nucleus and is a subunit of the cohesin complex which regulates the cohesion of sister chromatids during cell division. A mutation in this gene is associated with premature ovarian failure. Alternate splicing results in multiple transcript variants encoding distinct isoforms. This gene has multiple pseudogenes. [provided by RefSeq, Apr 2014]
Expression
Biased expression in testis (RPKM 44.6), brain (RPKM 6.1) and 2 other tissues See more
Orthologs
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Genomic context

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See STAG3 in Genome Data Viewer
Location:
7q22.1
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100177724..100219334)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101417534..101459147)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99775347..99812010)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99757927-99758426 Neighboring gene galactose-3-O-sulfotransferase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18425 Neighboring gene 60S ribosomal protein L29-like Neighboring gene glypican 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26345 Neighboring gene CASTOR family member 3, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26352 Neighboring gene PVR related immunoglobulin domain containing Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26353 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99844389-99845186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99845985-99846781 Neighboring gene uncharacterized LOC105375426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99866902-99867424 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99867949-99868470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18429 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:99886514-99886677 Neighboring gene speedy/RINGO cell cycle regulator family member E3 Neighboring gene PMS1 homolog 2, mismatch repair system component pseudogene 1

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. The upregulation of stromal antigen 3 expression suppresses the phenotypic hallmarks of hepatocellular carcinoma through the Smad3-CDK4/CDK6-cyclin D1 and CXCR4/RhoA pathways. Zhao M, et al. BMC Gastroenterol, 2022 Aug 8. PMID 35941537, Free PMC Article
  2. New STAG3 gene variant as a cause of premature ovarian insufficiency. Gómez-Rojas S, et al. Rev Colomb Obstet Ginecol, 2022 Mar 30. PMID 35503298, Free PMC Article
  3. A Long Contiguous Stretch of Homozygosity Disclosed a Novel STAG3 Biallelic Pathogenic Variant Causing Primary Ovarian Insufficiency: A Case Report and Review of the Literature. Mellone S, et al. Genes (Basel), 2021 Oct 27. PMID 34828315, Free PMC Article
  4. Biallelic loss of function variants in STAG3 result in primary ovarian insufficiency. Demain LAM, et al. Reprod Biomed Online, 2021 Nov. PMID 34497033
  5. Analysis of STAG3 variants in Chinese non-obstructive azoospermia patients with germ cell maturation arrest. Liu W, et al. Sci Rep, 2021 May 12. PMID 33980954, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. METTL3/IGF2BP2 axis affects the progression of colorectal cancer by regulating m6A modification of STAG3.
    Title: METTL3/IGF2BP2 axis affects the progression of colorectal cancer by regulating m6A modification of STAG3.
  2. The upregulation of stromal antigen 3 expression suppresses the phenotypic hallmarks of hepatocellular carcinoma through the Smad3-CDK4/CDK6-cyclin D1 and CXCR4/RhoA pathways.
    Title: The upregulation of stromal antigen 3 expression suppresses the phenotypic hallmarks of hepatocellular carcinoma through the Smad3-CDK4/CDK6-cyclin D1 and CXCR4/RhoA pathways.
  3. New STAG3 gene variant as a cause of premature ovarian insufficiency", trans "Nueva variante del gen STAG3 causante de insuficiencia ovarica prematura
    Title: New STAG3 gene variant as a cause of premature ovarian insufficiency.
  4. Biallelic loss of function variants in STAG3 result in primary ovarian insufficiency.
    Title: Biallelic loss of function variants in STAG3 result in primary ovarian insufficiency.
  5. A Long Contiguous Stretch of Homozygosity Disclosed a Novel STAG3 Biallelic Pathogenic Variant Causing Primary Ovarian Insufficiency: A Case Report and Review of the Literature.
    Title: A Long Contiguous Stretch of Homozygosity Disclosed a Novel STAG3 Biallelic Pathogenic Variant Causing Primary Ovarian Insufficiency: A Case Report and Review of the Literature.
  6. Analysis of STAG3 variants in Chinese non-obstructive azoospermia patients with germ cell maturation arrest.
    Title: Analysis of STAG3 variants in Chinese non-obstructive azoospermia patients with germ cell maturation arrest.
  7. STAG3 homozygous missense variant causes primary ovarian insufficiency and male non-obstructive azoospermia.
    Title: STAG3 homozygous missense variant causes primary ovarian insufficiency and male non-obstructive azoospermia.
  8. The meiosis-specific cohesin component stromal antigen 3 promotes cell migration and chemotherapeutic resistance in colorectal cancer.
    Title: The meiosis-specific cohesin component stromal antigen 3 promotes cell migration and chemotherapeutic resistance in colorectal cancer.
  9. The association of stromal antigen 3 (STAG3) sequence variations with spermatogenic impairment in the male Korean population.
    Title: The association of stromal antigen 3 (STAG3) sequence variations with spermatogenic impairment in the male Korean population.
  10. Mutations in the stromal antigen 3 (STAG3) gene cause male infertility due to meiotic arrest.
    Title: Mutations in the stromal antigen 3 (STAG3) gene cause male infertility due to meiotic arrest.
Submit: New GeneRIF Correction See all GeneRIFs (22)

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
Premature ovarian failure 8
MedGen: C3810367 OMIM: 615723 GeneReviews: Not available
Compare labs
Spermatogenic failure 61
MedGen: C5562048 OMIM: 619672 GeneReviews: Not available
not available

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in establishment of meiotic sister chromatid cohesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in establishment of meiotic sister chromatid cohesion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in establishment of meiotic sister chromatid cohesion NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in sister chromatid cohesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptonemal complex assembly TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular space HDA PubMed 
part_of meiotic cohesin complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of meiotic cohesin complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of meiotic cohesin complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
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 
located_in synaptonemal complex TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
cohesin subunit SA-3
Names
SCC3 homolog 3
stromal antigen 3
stromalin-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_034114.2 RefSeqGene

    Range
    5196..41659
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282716.1 → NP_001269645.1  cohesin subunit SA-3 isoform 1

    See identical proteins and their annotated locations for NP_001269645.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AA747738, AJ007798, BC146806
    Consensus CDS
    CCDS34703.1
    UniProtKB/Swiss-Prot
    A6H8Z1, B4DZ10, D6W5U8, H7BYK9, Q8NDP3, Q9UJ98
    UniProtKB/TrEMBL
    A8K8M9, B2RU25
    Related
    ENSP00000400359.1, ENST00000426455.5
    Conserved Domains (1) summary
    pfam08514
    Location:173 → 281
    STAG; STAG domain

  2. NM_001282717.2 → NP_001269646.1  cohesin subunit SA-3 isoform 2

    See identical proteins and their annotated locations for NP_001269646.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame acceptor splice site in the 3' coding region compared to variant 1. The resulting isoform (2) is 1 aa longer than isoform 1. Variants 3 and 5 both encode the same isoform (2).
    Source sequence(s)
    AC005071, AC073842
    Consensus CDS
    CCDS75642.1
    UniProtKB/TrEMBL
    A8K8M9, B2RU25, D6W5U7
    Related
    ENSP00000477973.1, ENST00000615138.5
    Conserved Domains (1) summary
    pfam08514
    Location:173 → 281
    STAG; STAG domain

  3. NM_001282718.2 → NP_001269647.1  cohesin subunit SA-3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks 2 consecutive in-frame exons in the 5' coding region compared to variant 1. The resulting shorter isoform (3) lacks an in internal protein segment compared to isoform 1.
    Source sequence(s)
    AA747738, AJ007798, AK302693, BC146806, DB097403
    Consensus CDS
    CCDS64730.1
    UniProtKB/TrEMBL
    A8K8M9, B2RU25
    Related
    ENSP00000484098.1, ENST00000620100.5
    Conserved Domains (1) summary
    pfam08514
    Location:115 → 223
    STAG; STAG domain

  4. NM_001375438.1 → NP_001362367.1  cohesin subunit SA-3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variant 3, encodes isoform 2.
    Source sequence(s)
    AC005071, AC073842
    Consensus CDS
    CCDS75642.1
    UniProtKB/TrEMBL
    A8K8M9, B2RU25, D6W5U7
    Conserved Domains (1) summary
    pfam08514
    Location:173 → 281
    STAG; STAG domain

  5. NM_012447.4 → NP_036579.2  cohesin subunit SA-3 isoform 1

    See identical proteins and their annotated locations for NP_036579.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AA747738, AJ007798, BC146806
    Consensus CDS
    CCDS34703.1
    UniProtKB/Swiss-Prot
    A6H8Z1, B4DZ10, D6W5U8, H7BYK9, Q8NDP3, Q9UJ98
    UniProtKB/TrEMBL
    A8K8M9, B2RU25
    Related
    ENSP00000319318.5, ENST00000317296.9
    Conserved Domains (1) summary
    pfam08514
    Location:173 → 281
    STAG; STAG domain

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    100177724..100219334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011685.2 → XP_016867174.2  cohesin subunit SA-3 isoform X1

  2. XM_047419788.1 → XP_047275744.1  cohesin subunit SA-3 isoform X4

    UniProtKB/TrEMBL
    D6W5U7

  3. XM_047419796.1 → XP_047275752.1  cohesin subunit SA-3 isoform X9

  4. XM_017011683.3 → XP_016867172.1  cohesin subunit SA-3 isoform X3

    UniProtKB/TrEMBL
    A8K8M9, B2RU25

  5. XM_047419787.1 → XP_047275743.1  cohesin subunit SA-3 isoform X1

  6. XM_047419786.1 → XP_047275742.1  cohesin subunit SA-3 isoform X1

  7. XM_017011686.3 → XP_016867175.2  cohesin subunit SA-3 isoform X2

  8. XM_047419797.1 → XP_047275753.1  cohesin subunit SA-3 isoform X10

  9. XM_047419792.1 → XP_047275748.1  cohesin subunit SA-3 isoform X6

  10. XM_017011687.2 → XP_016867176.2  cohesin subunit SA-3 isoform X7

  11. XM_017011684.2 → XP_016867173.2  cohesin subunit SA-3 isoform X1

  12. XM_047419793.1 → XP_047275749.1  cohesin subunit SA-3 isoform X6

  13. XM_047419789.1 → XP_047275745.1  cohesin subunit SA-3 isoform X4

    UniProtKB/TrEMBL
    D6W5U7

  14. XM_047419791.1 → XP_047275747.1  cohesin subunit SA-3 isoform X5

    UniProtKB/Swiss-Prot
    A6H8Z1, B4DZ10, D6W5U8, H7BYK9, Q8NDP3, Q9UJ98

  15. XM_047419795.1 → XP_047275751.1  cohesin subunit SA-3 isoform X9

  16. XM_047419790.1 → XP_047275746.1  cohesin subunit SA-3 isoform X5

    UniProtKB/Swiss-Prot
    A6H8Z1, B4DZ10, D6W5U8, H7BYK9, Q8NDP3, Q9UJ98

  17. XM_047419794.1 → XP_047275750.1  cohesin subunit SA-3 isoform X8

  18. XM_047419798.1 → XP_047275754.1  cohesin subunit SA-3 isoform X11

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    101417534..101459147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357109.1 → XP_054213084.1  cohesin subunit SA-3 isoform X1

  2. XM_054357112.1 → XP_054213087.1  cohesin subunit SA-3 isoform X4

    UniProtKB/TrEMBL
    D6W5U7

  3. XM_054357121.1 → XP_054213096.1  cohesin subunit SA-3 isoform X9

  4. XM_054357111.1 → XP_054213086.1  cohesin subunit SA-3 isoform X3

  5. XM_054357106.1 → XP_054213081.1  cohesin subunit SA-3 isoform X1

  6. XM_054357110.1 → XP_054213085.1  cohesin subunit SA-3 isoform X2

  7. XM_054357122.1 → XP_054213097.1  cohesin subunit SA-3 isoform X10

  8. XM_054357116.1 → XP_054213091.1  cohesin subunit SA-3 isoform X6

  9. XM_054357118.1 → XP_054213093.1  cohesin subunit SA-3 isoform X7

  10. XM_054357108.1 → XP_054213083.1  cohesin subunit SA-3 isoform X1

  11. XM_054357117.1 → XP_054213092.1  cohesin subunit SA-3 isoform X6

  12. XM_054357120.1 → XP_054213095.1  cohesin subunit SA-3 isoform X9

  13. XM_054357114.1 → XP_054213089.1  cohesin subunit SA-3 isoform X5

    UniProtKB/Swiss-Prot
    A6H8Z1, B4DZ10, D6W5U8, H7BYK9, Q8NDP3, Q9UJ98

  14. XM_054357119.1 → XP_054213094.1  cohesin subunit SA-3 isoform X8

  15. XM_054357115.1 → XP_054213090.1  cohesin subunit SA-3 isoform X5

    UniProtKB/Swiss-Prot
    A6H8Z1, B4DZ10, D6W5U8, H7BYK9, Q8NDP3, Q9UJ98

  16. XM_054357107.1 → XP_054213082.1  cohesin subunit SA-3 isoform X1

  17. XM_054357113.1 → XP_054213088.1  cohesin subunit SA-3 isoform X4

    UniProtKB/TrEMBL
    D6W5U7

  18. XM_054357123.1 → XP_054213098.1  cohesin subunit SA-3 isoform X11

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UJ98.2 GenPept UniProtKB/Swiss-Prot:Q9UJ98

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