FB2020_01, released Feb 12, 2020

Gene: Dmel\brv3

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General Information
Symbol
Dmel\brv3
Species
D. melanogaster
Name
brivido-3
Annotation Symbol
CG13762
Feature Type
protein_coding_gene
FlyBase ID
FBgn0040333
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Snapshot
In progress.Contributions welcome.
Other Summaries
Also Known As

EG:BACR7C10.7

Key Links
Genomic Location
Cytogenetic map
3A8-3A8
Sequence location
X:2,622,069..2,624,575 [-]
Recombination map

1-1

RefSeq locus
NC_004354 REGION:2622069..2624575
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
GO Summary Ribbons
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
calcium channel activity; calcium ion binding
Summaries
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\brv3 or the JBrowse view of Dmel\brv3 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 5.45

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
brv3-RB
FBtr0300708
NM_130657
2334
719
brv3-RC
FBtr0340092
NM_001297902
2427
750
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
brv3-PB
FBpp0289932
83.6
719
8.95
NP_570013
AAF45799
brv3-PC
FBpp0309091
87.1
750
8.85
NP_001284831
AHN59302
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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\brv3 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 (6 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
calcium channel activity
inferred from sequence or structural similarity
(Littleton and Ganetzky, 2000)
inferred from biological aspect of ancestor with PANTHER:PTN000093539
(assigned by GO_Central )
(Gaudet et al., 2011)
calcium ion binding
inferred from electronic annotation with InterPro:IPR003915
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
response to cold
inferred from mutant phenotype
(Gallio et al., 2011)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
calcium ion transport
inferred from sequence or structural similarity
(Littleton and Ganetzky, 2000)
detection of mechanical stimulus
inferred from biological aspect of ancestor with PANTHER:PTN000093539
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
membrane
inferred from biological aspect of ancestor with PANTHER:PTN000093539
(assigned by GO_Central )
(Gaudet et al., 2011)
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
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\brv3 in GBrowse 2
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
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
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 0 )
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 brv3
Transgenic constructs containing regulatory region of brv3
Deletions and Duplications ( 0 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4e22c, Scer\GAL4sqh.PW
Other Phenotypes
Allele
cold stress response defective, with Scer\GAL4scrt-11-6
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (7)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\PKD2L1
3 of 15
Yes
No
 
Hsap\PKD2L2
3 of 15
Yes
No
Hsap\PKD1L1
2 of 15
No
Yes
Hsap\PKD1L2
1 of 15
No
No
Hsap\PKD1L3
1 of 15
No
No
Hsap\PKD2
1 of 15
No
No
Hsap\PKDREJ
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (8)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Pkd2l1
3 of 15
Yes
No
Mmus\Pkd2l2
3 of 15
Yes
No
Mmus\Pkd1l1
2 of 15
No
Yes
Mmus\Pkd1l2
1 of 15
No
No
Mmus\Pkd1l3
1 of 15
No
No
Mmus\Pkd1
1 of 15
No
No
Mmus\Pkd2
1 of 15
No
No
Mmus\Pkdrej
1 of 15
No
No
Rattus norvegicus (Norway rat) (8)
Rnor\Pkd2l1
3 of 13
Yes
No
Rnor\Pkd2l2
3 of 13
Yes
No
Rnor\LOC100362565
1 of 13
No
No
Rnor\Pkd1l1
1 of 13
No
Yes
Rnor\Pkd1l2
1 of 13
No
No
Rnor\Pkd1
1 of 13
No
No
Rnor\Pkd2
1 of 13
No
No
Rnor\Pkdrej
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\pkd1
1 of 12
Yes
Yes
Xtro\pkd2l1
1 of 12
Yes
Yes
Danio rerio (Zebrafish) (5)
Drer\pkd2
2 of 15
Yes
No
Drer\pkd2l1
2 of 15
Yes
No
Drer\LOC100537993
1 of 15
No
No
Drer\pkd1a
1 of 15
No
Yes
Drer\pkd1b
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\pkd-2
3 of 15
Yes
No
Cele\lov-1
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091903IY )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\brv3
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00004666
Drosophila simulans
Dsim\GD27606
Drosophila sechellia
Dsec\GM18868
Drosophila erecta
Dere\GG12602
Drosophila yakuba
Dyak\GE16933
Drosophila ananassae
Dana\GF21928
Drosophila pseudoobscura pseudoobscura
Dpse\GA23663
Drosophila persimilis
Dper\GL26193
Drosophila willistoni
Dwil\GK16275
Drosophila virilis
Dvir\GJ11886
Drosophila mojavensis
Dmoj\GI13528
Drosophila mojavensis
Dmoj\GI13527
Drosophila grimshawi
Dgri\GH14404
Drosophila grimshawi
Dgri\GH14405
Drosophila grimshawi
Dgri\GH14403
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091502TR )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17024336
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07201
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02L5 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Tribolium castaneum
Red flour beetle
Tcas\TC012839
Tribolium castaneum
Red flour beetle
Tcas\TC034437
Tribolium castaneum
Red flour beetle
Tcas\TC001937
Tribolium castaneum
Red flour beetle
Tcas\TC012838
Pediculus humanus
Human body louse
Phum\PHUM245520
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_09058
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
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (3)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
brv2
4 of 10
brv1
3 of 10
Pkd2
2 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 ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    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.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    PKD2L1; polycystin 2 like 1, transient receptor potential cation channel
    3 of 15
    604532
         
        PKD2L2; polycystin 2 like 2, transient receptor potential cation channel
        3 of 15
        604669
            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
            Interactions Browser
            Summary of Genetic Interactions
            esyN Network Diagram
            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.
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            Pathways
            Signaling Pathways (FlyBase)
            Metabolic Pathways
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            X
            Recombination map

            1-1

            Cytogenetic map
            3A8-3A8
            Sequence location
            X:2,622,069..2,624,575 [-]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            3A8-3A8
            Limits computationally determined from genome sequence between P{EP}eghEP804 and P{EP}sggEP1576
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location

            1-1

            (FlyBase, 2016)

            1-1.2

            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (5)
            Genomic Clones (13)
             

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

            cDNA Clones (3)
             

            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)
            BDGP DGC clones
            Other 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: brv3 CG13762

              (Gallio et al., 2011)
              Source for database merge of

              Source for merge of: EG:BACR7C10.7 CG13762

              (FlyBase, 1996-)
              Additional comments

              Source for merge of EG:BACR7C10.7 CG13762 was sequence comparison ( date:000425 ).

              (FlyBase, 1996-)
              Other Comments
              Origin and Etymology
              Discoverer
              Etymology

              'brivido' is Italian for shiver, and mutants are deficient in sensing cold temperature.

              (Gallio et al., 2011)
              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
              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
              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
              Linkouts
              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
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              FlyMine - An integrated database for Drosophila genomics
              InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
              Synonyms and Secondary IDs (8)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              References (26)