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General Information
Symbol
Dmel\Snr1
Species
D. melanogaster
Name
Snf5-related 1
Annotation Symbol
CG1064
Feature Type
FlyBase ID
FBgn0011715
Gene Model Status
Stock Availability
Gene Snapshot
Snf5-related 1 (Snr1) encodes a core component of the ATP-dependent SWI/SNF chromatin-remodeling complex (Brahma complex). It functions as a tumor suppressor and is required for maintaining normal endosomal trafficking-mediated signaling cascades. [Date last reviewed: 2018-09-13]
Also Known As
BAP45
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:5,470,926..5,472,754 [+]
Recombination map
3-47.5
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Molecular Function (GO)
[Detailed GO annotations]
Summaries
Gene Group (FlyBase)
BRAHMA ASSOCIATED PROTEINS COMPLEX -
Brahma (BRM) complexes are ATP-dependent chromatin remodeling complexes that regulate nucleosome organization. Two BRM complexes have been identified in D.mel, BAP and PBAP. (Adapted from FBrf0192510).
POLYBROMO-CONTAINING BRAHMA ASSOCIATED PROTEINS COMPLEX -
Brahma (BRM) complexes are ATP-dependent chromatin remodeling complexes that regulate nucleosome organization. Two BRM complexes have been identified in D.mel, BAP and PBAP. (Adapted from FBrf0192510).
Summary (Interactive Fly)
a component of the Swi/Snf complex (Brahma complex) in Drosophila - suppresses mutations in Polycomb complex genes - a tumor suppressor in imaginal tissues
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\Snr1 or the JBrowse view of Dmel\Snr1 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
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.49
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0078682
1335
370
Additional Transcript Data and Comments
Reported size (kB)
1.4 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0078331
41.9
370
4.91
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)
370 (aa); 43 (kD observed); 43 (kD predicted)
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\Snr1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (22 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:brm; FB:FBgn0000212
inferred from physical interaction with FLYBASE:CycE; FB:FBgn0010382
inferred from physical interaction with FLYBASE:Rbf; FB:FBgn0015799
inferred from physical interaction with FLYBASE:trx; FB:FBgn0003862
inferred from physical interaction with UniProtKB:Q9VQ56
(assigned by UniProt )
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000797502
(assigned by GO_Central )
Biological Process (12 terms)
Terms Based on Experimental Evidence (10 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with SGD:S000005816
inferred from biological aspect of ancestor with PANTHER:PTN000001217
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000001217
(assigned by GO_Central )
Cellular Component (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000797502
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000797502
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000797502
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000001217
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000001217
(assigned by GO_Central )
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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

antennal primordium

Comment: reported as procephalic ectoderm primordium

central brain primordium

Comment: reported as procephalic ectoderm primordium

visual primordium

Comment: reported as procephalic ectoderm primordium

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Nothern blotting with Snr1 specific riboprobes confirmed that the transcript can be detected at all stages of development. A transient increase in message was observed late in third instar larvae and in pupae corresponding to the time of rising titers of ecdysone hormone. In contrast to previous experiments expression was detected in adult males.
Snr1 transcripts are expressed maximally in unfertilized eggs and early embryos, indicating maternal contributions. Levels drop steadily during embryogenesis with a dramatic drop at 16hrs. Low levels of Snr1 transcripts are observed in larvae, pupae, and adult females. The temporal pattern of Snr1 transcription is very similar to that of brm.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
organism
nucleus

Comment: punctate within nuclei in a restricted region near the posterior

western blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Fluorescent confocal imaging of Snr1 localization in similarly staged embryos showed that the protein was tightly associated with chromatin in the vast majority of nuclei. Occasionally, Snr1 appeared more diffuse in the cytosol and closer examination revealed that the majority of chromosomes were in metaphase.
In the larval CNS expression of Snr1 protein is restricted to a subset of cells in the optic lobe. The protein is also restricted to subsets of cells in the leg and wing discs with low or undetectable expression in some discs. The Snr1 protein is detected at relatively high levels in developing eye discs both anterior and posterior to the morphogenetic furrow. The protein is detected in a punctate pattern within the nuclei of salivary gland cells. Staining is also observed in germarium regions 2 and 3 in the ovariole. A few cells of the somatic follicular sheath and nurse cell nuclei and the developing oocyte also express low levels of the Snr1 protein.
Snr1 protein is detected at its highest level in early embryos. Low levels are found in larvae, pupae, and adult females. Snr1 protein is found in all nuclei of the embryo through germ band extension. After germ band retraction it is located almost exclusively in the brain and CNS. Snr1 protein is detected in salivary glands and imaginal discs in larvae
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Snr1 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
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
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 13 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 17 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Snr1
Transgenic constructs containing regulatory region of Snr1
Deletions and Duplications ( 4 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
adult thorax | dorsal & chaeta | somatic clone
mechanosensory chaeta & adult abdomen | somatic clone
mechanosensory chaeta | supernumerary & adult abdomen | somatic clone
socket & adult abdomen | somatic clone
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (2)
8 of 13
Yes
Yes
7 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (1)
11 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
13 of 15
Yes
Yes
8 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
13 of 15
Yes
Yes
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (1)
6 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
10 of 15
Yes
Yes
9 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
8 of 12
Yes
Yes
7 of 12
No
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190AZY )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
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 mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091506FQ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W06OE )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X06Y8 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0AOO )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (0)
No records found.
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 3 )
Potential Models Based on Orthology ( 3 )
Modifiers Based on Experimental Evidence ( 1 )
Allele
Disease
Interaction
References
Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
 
Disease Associations of Human Orthologs (via DIOPT v7.1 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
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Gene Group - Pathway Membership (FlyBase)
External Data
Linkouts
SignaLink - A signaling pathway resource with multi-layered regulatory networks.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3R
Recombination map
3-47.5
Cytogenetic map
Sequence location
3R:5,470,926..5,472,754 [+]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
83A4-83A4
Limits computationally determined from genome sequence between P{EP}EP974 and P{PZ}Snr101319&P{PZ}Itp-r83A05616
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
83A5-83A6
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (8)
Genomic Clones (21)
cDNA Clones (47)
 

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 sequences
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)
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: Snr1 CG1064
Source for database merge of
Additional comments
Other Comments
dsRNA has been made from templates generated with primers directed against this gene. RNAi of Snr1 results in dorsal overextension of primary dendrites and a reduction in lateral branching. RNAi also causes defects in muscle, defects in the epidermis, defects in dendrite morphogenesis and reproducible defects in da dendrite development.
Loss of Snr1 function results in ectopic vein material in the wing.
Snr1 is identified in a yeast two-hybrid screen for proteins interacting with trx. Yeast two-hybrid assays, in vitro binding assays and coimmunoprecipitation of proteins from cultured cells and transgenic flies demonstrates the trx and Snr1 proteins interact.
The Snr1 and brm proteins are present in a large complex and co-precipitate from extracts, these results suggest that the Drosophila counterpart of the yeast SWI/SNF complex plays an important role in counteracting the repressive effects of chromatin on homeotic gene transcription during development.
Snr1 is essential for viability. Phenotypic studies and genetic interactions suggest that Snr1 and brm act together, and with trx, to regulate homeotic gene transcription. Snr1 and brm proteins are present in a large complex, this complex may play an important role in maintaining homeotic gene transcription during development by counteracting the repressive effect of chromatin.
Origin and Etymology
Discoverer
Etymology
Identification
External Crossreferences and Linkouts ( 38 )
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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
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
iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
InterPro - A database of protein families, domains and functional sites
KEGG Genes - Molecular building blocks of life in the genomic space.
modMine - A data warehouse for the modENCODE project
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
SignaLink - A signaling pathway resource with multi-layered regulatory networks.
Linkouts
BioGRID - A database of protein and genetic interactions.
DPiM - Drosophila Protein interaction map
DroID - A comprehensive database of gene and protein interactions.
DRSC - Results frm RNAi screens
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyMine - An integrated database for Drosophila genomics
Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
MIST (genetic) - An integrated Molecular Interaction Database
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 (13)
Reported As
Symbol Synonym
l(3)01319
Secondary FlyBase IDs
  • FBgn0010744
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
References (159)