FB2024_04 , released June 25, 2024
Gene: Dmel\Tmc
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General Information
Symbol
Dmel\Tmc
Species
D. melanogaster
Name
Transmembrane channel-like
Annotation Symbol
CG46121
Feature Type
FlyBase ID
FBgn0267796
Gene Model Status
Stock Availability
Gene Summary
Transmembrane channel-like (Tmc) encodes a protein involved in proprioception and locomotory behavior in larvae. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)
Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-31
RefSeq locus
NT_037436 REGION:9597764..9614001
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (12 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
Biological Process (9 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
involved_in proprioception
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in dendrite
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in plasma membrane
inferred from electronic annotation with InterPro:IPR038900
Protein Family (UniProt)
Belongs to the TMC family. (A0A0U1QT59)
Summaries
Gene Snapshot
Transmembrane channel-like (Tmc) encodes a protein involved in proprioception and locomotory behavior in larvae. [Date last reviewed: 2019-09-19]
Gene Group (FlyBase)
TRANSMEMBRANE CHANNEL-LIKE FAMILY SUBUNITS -
Transmembrane channel-like proteins are putative mechanically-activated, non-selective cation channels. (Adapted from PMID:37543036 and FBrf0246684.)
Protein Function (UniProtKB)
Probable ion channel (PubMed:27478019, PubMed:30853433, PubMed:31184585, PubMed:32649914). Component of mechanosensitive neurons that participates in proprioception, sensing food texture, and directing egg-laying site selection (oviposition) (PubMed:27298354, PubMed:27478019, PubMed:30853433, PubMed:31184585, PubMed:32649914). Component of multi-dendritic neurons of the labellum (md-L) where it is required for sensing the hardness and viscosity of their food, enabling them to behaviorally discriminate their preferred softness and smoothness from harder and stickier food options (PubMed:27478019). Required as part of oviposition site selection process to relay mechanosensory and chemosensory information on the hardness and sweetness of potential egg-laying substrates, thus ensuring females select the most optimal site for their eggs survival (PubMed:31184585, PubMed:32649914). Females determine the softest substrate for their eggs first by making a coarse evaluation of substrate hardness using mechanosensitive channels nan and Piezo in the leg tarsal bristles, followed by a much finer assessment using nan, iav and Tmc mechanosensitive channels on the labellum (PubMed:31184585, PubMed:32649914). This protein is required to sense subtle differences in substrate stiffness (between 0.25% and 0.3% agarose), likely acting in the md-L neurons (PubMed:32649914). Also required in neurons on the labellum, including the md-Ls, and possibly in the brain, to inhibit discrimination of egg-laying substrates of different hardness if the substrate contains sucrose (PubMed:32649914). During oviposition evaluation, activation of sweet neurons by sucrose enhances the activity of the Tmc neurons resulting in females losing their softness preference in favor of egg-laying sites that contain sucrose (PubMed:32649914). Acts in the larvae peripheral sensory neurons, to contribute to proprioception and sensory feedback for normal forward crawling behavior (PubMed:27298354, PubMed:30853433). Required for the normal activity of the proprioceptive sensory dendrites, ddaE which show preferential responses to forward locomotion, and ddaD which show preferential responses to backward locomotion (PubMed:30853433).
(UniProt, A0A0U1QT59)
Summary (Interactive Fly)

larval proprioception - defensive response to mechanical stimuli - Tmc cells undergo restructuring engendering an enhanced response to touching in females following mating - critical for sensing subtle differences in substrate stiffness during ovoposition - required for sensing two key textural features of food-hardness and viscosity - presumably activated by membrane curvature in dendrites that are exposed to strain

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Tmc 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 A0A0U1QT59)

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 6.02

Alternative transcript with retained intron postulated (between exons 4 and 5 of transcript -RA; FBrf0180668).

Gene model reviewed during 6.04

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0347573
6398
2036
FBtr0347574
6349
1932
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
FBpp0312604
227.3
2036
6.59
FBpp0312605
216.7
1932
6.53
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\Tmc 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).

-0.84

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in dendrite
inferred from mutant phenotype
Expression Deduced from Reporters
Reporter: P{Tmc-GAL4.3.0}
Stage
Tissue/Position (including subcellular localization)
Reference
Reporter: P{Tmc-GAL4.G}
Stage
Tissue/Position (including subcellular localization)
Reference
Reporter: P{Tmc-QF.3.0}
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Tmc in JBrowse
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
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
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 7 )
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 Tmc
Transgenic constructs containing regulatory region of Tmc
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (8)
9 of 14
Yes
Yes
8 of 14
No
Yes
8 of 14
No
Yes
2 of 14
No
Yes
2 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (8)
9 of 14
Yes
Yes
8 of 14
No
Yes
8 of 14
No
Yes
2 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
Mus musculus (laboratory mouse) (8)
9 of 14
Yes
Yes
8 of 14
No
Yes
8 of 14
No
Yes
2 of 14
No
Yes
2 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (7)
5 of 13
Yes
Yes
5 of 13
Yes
Yes
5 of 13
Yes
No
2 of 13
No
Yes
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
Yes
Danio rerio (Zebrafish) (9)
10 of 14
Yes
Yes
10 of 14
Yes
Yes
10 of 14
Yes
Yes
2 of 14
No
Yes
2 of 14
No
Yes
2 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
9 of 14
Yes
Yes
9 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (3)
8 of 12
Yes
Yes
8 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Tmc. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
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 ( 2 )
    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.
    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
    Other Interaction Browsers
    Summary of Genetic Interactions
    esyN Network Diagram
    Other Interaction Browsers
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-31
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    67C2-67C2
    Limits computationally determined from genome sequence between P{EP}Hsp26EP3336&P{EP}Hsp26EP3315 and P{PZ}fry02240
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (17)
    Genomic Clones (31)
    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 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
              Antibody Information
              Laboratory Generated Antibodies
              Commercially Available Antibodies
               
              Cell Line Information
              Publicly Available Cell Lines
               
                Other Stable Cell Lines
                 
                  Other Comments

                  Tmc is required for sensing the hardness and viscosity of food.

                  Relationship to Other Genes
                  Source for database merge of

                  Source for merge of: CG14177 CG3280

                  Additional comments

                  Annotations CG14177 and CG3280 merged as CG46121 in release 6.03 of the genome annotation. Merge supported by RNA-Seq coverage and exon junction data.

                  Nomenclature History
                  Source for database identify of

                  Source for identity of: Tmc CG46121

                  Nomenclature comments
                  Etymology

                  Named 'Transmembrane channel-like' (Tmc) after the mammalian orthologs.

                  Synonyms and Secondary IDs (12)
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  Study result (0)
                  Result
                  Result Type
                  Title
                  External Crossreferences and Linkouts ( 26 )
                  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/Swiss-Prot - Manually annotated and reviewed 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
                  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
                  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
                  iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                  Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
                  References (63)