FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\SA1
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General Information
Symbol
Dmel\SA1
Species
D. melanogaster
Name
Stromalin 1
Annotation Symbol
CG3423
Feature Type
protein_coding_gene
FlyBase ID
FBgn0020616
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Summary
Stromalin 1 (SA1) encodes a subunit of the cohesin ring complex, which encircles sister chromatids after DNA replication and has multiple roles in the regulation of gene expression and DNA repair. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

SA, Stromalin, SCC3, DSA1, DmSA

Key Links
Genomic Location
Cytogenetic map
27C7-27C7
Sequence location
Recombination map
2-23
RefSeq locus
NT_033779 REGION:6950421..6954586
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (13 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables chromatin binding
inferred from direct assay
(Misulovin et al., 2008)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables chromatin binding
inferred from sequence or structural similarity with SGD:S000001288
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(GO Reference Genome Project, 2011-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in neuron remodeling
inferred from mutant phenotype
(Schuldiner et al., 2008)
involved_in synaptonemal complex assembly
inferred from mutant phenotype
(Gyuricza et al., 2016)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in mitotic sister chromatid cohesion
inferred from sequence or structural similarity with SGD:S000001288
(Gene Ontology Curators, 2002-)
involved_in sister chromatid cohesion
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(GO Reference Genome Project, 2011-)
Cellular Component (8 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
part_of cohesin complex
inferred from direct assay
(Gause et al., 2008)
located_in condensed chromosome, centromeric region
inferred from direct assay
(Valdeolmillos et al., 2004)
located_in euchromatin
inferred from direct assay
(Misulovin et al., 2008)
located_in pericentric heterochromatin
inferred from direct assay
(Valdeolmillos et al., 2004)
located_in spindle pole
inferred from direct assay
(Valdeolmillos et al., 2004)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
is_active_in chromatin
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(GO Reference Genome Project, 2011-)
part_of cohesin complex
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(GO Reference Genome Project, 2011-)
part_of mitotic cohesin complex
inferred from sequence or structural similarity with SGD:S000001288
(Gene Ontology Curators, 2002-)
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Stromalin 1 (SA1) encodes a subunit of the cohesin ring complex, which encircles sister chromatids after DNA replication and has multiple roles in the regulation of gene expression and DNA repair. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
MITOTIC COHESIN COMPLEX -
The mitotic cohesin complex forms a ring-like structure which encircles sister chromatids holding them together after mitotic DNA replication. (Adapted from FBrf0207490).
MEIOTIC COHESIN COMPLEX C2M-SA VARIANT -
The meiotic cohesin complex forms a ring-like structure which encircles sister chromatids holding them together after meiotic DNA replication. (Adapted from FBrf0232850.)
Summary (Interactive Fly)

component of cohesin ring complex - regulates meiotic sister chromatid cohesion - important for chromosome condensation, DNA repair, and gene expression - negative regulator of synaptic vesicle pool size in dopamine neurons

Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\SA1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VM62)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.52

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
SA1-RA
FBtr0079349
NM_057920
3634
1127
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
SA1-PA
FBpp0078977
130.1
1127
5.06
Q9VM62
NP_477268
AAF52463
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\SA1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-1.07

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of cohesin complex
inferred from direct assay
(Gause et al., 2008)
located_in condensed chromosome, centromeric region
inferred from direct assay
(Valdeolmillos et al., 2004)
located_in euchromatin
inferred from direct assay
(Misulovin et al., 2008)
located_in pericentric heterochromatin
inferred from direct assay
(Valdeolmillos et al., 2004)
located_in spindle pole
inferred from direct assay
(Valdeolmillos et al., 2004)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\SA1 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of SA1
Transgenic constructs containing regulatory region of SA1
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2L)Exel7029
(Ryder, 2004.4.26)
Inferred from location ( 4 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (8)
Hsap\STAG1
14 of 14
Yes
Yes
Hsap\STAG2
13 of 14
No
Yes
Hsap\STAG3
13 of 14
No
Yes
Hsap\STAG3L1
2 of 14
No
Yes
Hsap\STAG3L2
2 of 14
No
Yes
Hsap\STAG3L3
2 of 14
No
Yes
Hsap\STAG3L4
2 of 14
No
Yes
Hsap\TRIM74
1 of 14
No
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (3)
Rnor\Stag1
14 of 14
Yes
Yes
Rnor\Stag2
13 of 14
No
Yes
Rnor\Stag3
13 of 14
No
Yes
Mus musculus (laboratory mouse) (3)
Mmus\Stag1
14 of 14
Yes
Yes
Mmus\Stag2
13 of 14
No
Yes
Mmus\Stag3
12 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (9)
Xtro\stag1
11 of 13
Yes
Yes
Xtro\stag2
10 of 13
No
Yes
Xtro\nags
9 of 13
No
Yes
Xtro\stag3
7 of 13
No
Yes
Xtro\LOC100486631
6 of 13
No
Yes
Xtro\ptpn21
2 of 13
No
No
Xtro\atg16l1
1 of 13
No
No
Xtro\snupn
1 of 13
No
No
Xtro\timm23
1 of 13
No
No
Danio rerio (Zebrafish) (6)
Drer\stag1a
14 of 14
Yes
Yes
Drer\stag1b
14 of 14
Yes
Yes
Drer\stag2a
13 of 14
No
Yes
Drer\stag2b
13 of 14
No
Yes
Drer\si:ch211-269e2.1
10 of 14
No
Yes
Drer\LOC100333021
4 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\scc-3
13 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP006998
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\SCC3
13 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\IRR1
7 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\psc3
8 of 12
Yes
Yes
Spom\rec11
3 of 12
No
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:SA1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
SA2
9 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 0 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 5 )
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
Homo sapiens (Human)
Gene name
Score
OMIM
OMIM Phenotype
DO term
Complementation?
Transgene?
STAG1; STAG1 cohesin complex component
14 of 14
604358
STAG2; STAG2 cohesin complex component
13 of 14
300826
STAG3; STAG3 cohesin complex component
13 of 14
608489
Functional Complementation Data
Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
Interactions
Summary of Physical Interactions
Summary of Genetic Interactions
Interaction Browsers
View in FlyBase Interactions Browser   View in MIST tool (external link)
Please look at the allele data for full details of the genetic interactions
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
ct
suppressible
SA1
(Rollins et al., 2004)
External Data
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
FlyBase
External Links
External Data
Linkouts
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-23
Cytogenetic map
27C7-27C7
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
27C7-27C7
Limits computationally determined from genome sequence between P{lacW}xl6k00230&P{EP}Hrb27CEP748 and P{PZ}smt304841&P{PZ}smt304493
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
27C-27C
(determined by in situ hybridisation)
(Valdeolmillos et al., 1998, EDGP Project Members, 1994-)
Experimentally Determined Recombination Data
Location

2-23

(FlyBase, 2016)

2-22.2

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (8)
Genomic Clones (20)
cDNA Clones (28)
 

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced
BDGP DGC clones
Other clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
     

    polyclonal

    (Phan et al., 2019, Moshkin et al., 2013, Dorsett et al., 2005)
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments
        Relationship to Other Genes
        Source for database merge of
        Additional comments
        Nomenclature History
        Source for database identify of

        Source for identity of: SA CG3423

        (Wortman, 1999.11)

        Source for identity of: SA1 SA

        (Valdeolmillos et al., 2004)
        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (14)
        Reported As
        Symbol Synonym
        CG3423
        (Glittenberg et al., 2022, Meadows, 2017.1.11, Çiçek et al., 2016, Christis and Munro, 2012, Ni et al., 2011.7.19, Lunardi et al., 2010, Ni et al., 2010.12.1, Keleman et al., 2009.8.5)
        DSA
        (Valdeolmillos et al., 1998)
        DSA1
        (Savvidou et al., 2005, Valdeolmillos et al., 2004)
        DmSA
        (Haering and Nasmyth, 2003, Hirano, 2002)
        ESTS:92H2T
        SA
        (Vallés et al., 2024, Horsfield, 2023, Kaushal et al., 2022, Bilder et al., 2021, Kaushal et al., 2021, Wolfe et al., 2021, Galander and Marston, 2020, Meyer-Nava et al., 2020, Arya et al., 2019, King et al., 2019, Phan et al., 2019, Pherson et al., 2019, Gene Disruption Project members, 2018-, Hughes et al., 2018, Misulovin et al., 2018, Dorsett, 2016, Gyuricza et al., 2016, Ribeiro et al., 2016, Senaratne et al., 2016, Swain et al., 2016, Kusch, 2015, Chen et al., 2014, Gonzalez et al., 2014, Krishnan et al., 2014, Oliveira et al., 2014, Weng et al., 2014, Moshkin et al., 2013, Carter and Sjögren, 2012, Fasulo et al., 2012, Japanese National Institute of Genetics, 2012.5.21, McKee et al., 2012, Gause et al., 2010, Macalpine et al., 2010, Dorsett, 2009, Moshkin et al., 2009, Schaaf et al., 2009, Gause et al., 2008, Misulovin et al., 2008, Pauli et al., 2008, Schuldiner et al., 2008, Mukai et al., 2006, Rollins et al., 2004, Cayirlioglu et al., 2003)
        SA-1
        (Monribot-Villanueva et al., 2017)
        SA1
        (Carmo et al., 2023, Canales Coutiño et al., 2020)
        SCC3
        (McKee et al., 2012, Mouri et al., 2012, McKim, 2005, Khetani and Bickel, 2002)
        Scc3
        (Dorsett et al., 2005, Rollins et al., 2004)
        stromalin
        (Matthews and White, 2019)
        Name Synonyms
        Stromalin
        (Noyes et al., 2021, Fellmeth and McKim, 2020, Gyuricza et al., 2016, Senaratne et al., 2016, Jeppsson et al., 2014, McKee et al., 2012, Bartkuhn et al., 2009, Dorsett, 2009, Schaaf et al., 2009, Schuldiner et al., 2008, Mukai et al., 2006, Dorsett et al., 2005, Valdeolmillos et al., 1998)
        Stromalin 1
        cohesin
        (Schaaf et al., 2009)
        stromalin
        (Davis, 2023, Krishnan et al., 2014, Oliveira et al., 2014, Moshkin et al., 2013, Fasulo et al., 2012, Mouri et al., 2012, Rollins et al., 2004)
        Secondary FlyBase IDs
        • FBgn0020933
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 43 )
        Sequence Crossreferences
        NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
        GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
        GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
        UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Other crossreferences
        AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
        DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
        EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        FlyMine - An integrated database for Drosophila genomics
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        References (101)