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General Information
Symbol
Dmel\SA-2
Species
D. melanogaster
Name
Stromalin-2
Annotation Symbol
CG13916
Feature Type
FlyBase ID
FBgn0043865
Gene Model Status
Stock Availability
Gene Summary
Stromalin-2 (SA-2) encodes a paralog of the cohesin protein encoded by SA. It functions in the male meiosis-specific homolog pairing pathway. It is required to maintain homolog pairing and to ensure bi-orientation of homologs during meiosis I. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
Also Known As

snm, pf-1, stromalin in meiosis

Key Links
Genomic Location
Cytogenetic map
Sequence location
3L:1,434,336..1,437,872 [-]
Recombination map
3-0.5
RefSeq locus
NT_037436 REGION:1434336..1437872
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(assigned by GO_Central )
Biological Process (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(assigned by GO_Central )
Cellular Component (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
colocalizes_with condensed chromosome
inferred from direct assay
inferred from direct assay
colocalizes_with nucleolus
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
is_active_in chromatin
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(assigned by GO_Central )
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000127652
(assigned by GO_Central )
Gene Group (FlyBase)
Protein Family (UniProt)
-
Summaries
Gene Snapshot
Stromalin-2 (SA-2) encodes a paralog of the cohesin protein encoded by SA. It functions in the male meiosis-specific homolog pairing pathway. It is required to maintain homolog pairing and to ensure bi-orientation of homologs during meiosis I. [Date last reviewed: 2019-03-14]
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\SA-2 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
Comments on Gene Model

Gene model reviewed during 5.50

Gene model reviewed during 5.42

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0301788
3219
973
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
RefSeq ID
GenBank
FBpp0291002
110.9
973
6.07
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\SA-2 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
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
colocalizes_with condensed chromosome
inferred from direct assay
inferred from direct assay
colocalizes_with nucleolus
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\SA-2 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
EMBL-EBI Single Cell Expression Atlas
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
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 SA-2
Transgenic constructs containing regulatory region of SA-2
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (8)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
7 of 15
Yes
No
7 of 15
Yes
No
7 of 15
Yes
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
7 of 15
Yes
No
7 of 15
Yes
No
6 of 15
No
No
Rattus norvegicus (Norway rat) (4)
6 of 13
Yes
No
5 of 13
No
No
5 of 13
No
No
2 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
5 of 12
Yes
No
5 of 12
Yes
Yes
2 of 12
No
Yes
2 of 12
No
Yes
Danio rerio (Zebrafish) (6)
7 of 15
Yes
No
7 of 15
Yes
No
7 of 15
Yes
No
6 of 15
No
No
2 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
7 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (1)
4 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
4 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
3 of 12
Yes
No
2 of 12
No
No
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091905D5 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila virilis
Drosophila mojavensis
Drosophila mojavensis
Drosophila grimshawi
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( None identified )
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
5 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 0 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 3 )
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
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
esyN Network Diagram
Show neighbor-neighbor interactions:
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Interactions Browser

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
esyN Network Diagram
esyN Network Key:
Suppression
Enhancement

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
External Data
Linkouts
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3L
Recombination map
3-0.5
Cytogenetic map
Sequence location
3L:1,434,336..1,437,872 [-]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
62A1-62A1
Limits computationally determined from genome sequence between P{PZ}l(3)0264002640 and P{EP}rhoEP3704&P{PZ}l(3)0622606226
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Localised using deficiency mapping (details unspecified).
Localised by deficiency and genetic mapping (details unspecified).
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (3)
Genomic Clones (15)
 

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (2)
 

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 GBrowse 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
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of

      Source for identity of: SA-2 pf-1

      Source for identity of: SA-2 SNM

      Source for database merge of

      Source for merge of: SA-2 anon-WO0109301.35

      Additional comments

      Source for merge of SA-2 anon-WO0109301.35 was sequence comparison ( date:051113 ).

      Other Comments

      SA-2 has a role in the maintenance of homologous chromosome pairing in meiosis.

      Mutant testes show unpaired chromosomes at prophase and metaphase I and "laggard chromosomes" at anaphase I in meiotic cells.

      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 37 )
      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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      EMBL-EBI Single Cell Expression Atlas
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL
      modMine - A data warehouse for the modENCODE project
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      FlyMine - An integrated database for Drosophila genomics
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Synonyms and Secondary IDs (12)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (48)