FB2024_04 , released June 25, 2024
Gene: Dmel\up
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General Information
Symbol
Dmel\up
Species
D. melanogaster
Name
upheld
Annotation Symbol
CG7107
Feature Type
FlyBase ID
FBgn0004169
Gene Model Status
Stock Availability
Gene Summary
upheld (up) encodes the striated muscle protein Troponin T. Troponins T, C and I form a regulatory complex with Tropomyosin that is found at regular intervals along the thin (F-actin) filaments of the muscle sarcomere. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)
Also Known As

TnT, troponin T, TpnT, troponin-T, int

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-44
RefSeq locus
NC_004354 REGION:13593474..13602578
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (15 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000162487
Biological Process (11 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from expression pattern
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in muscle contraction
inferred from biological aspect of ancestor with PANTHER:PTN000162487
inferred from electronic annotation with InterPro:IPR027707
inferred from biological aspect of ancestor with PANTHER:PTN000162487
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001978, InterPro:IPR027707
inferred from biological aspect of ancestor with PANTHER:PTN000162487
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the troponin T family. (P19351)
Summaries
Gene Snapshot
upheld (up) encodes the striated muscle protein Troponin T. Troponins T, C and I form a regulatory complex with Tropomyosin that is found at regular intervals along the thin (F-actin) filaments of the muscle sarcomere. [Date last reviewed: 2019-03-21]
Gene Group (FlyBase)
TROPONIN T ISOFORMS -
The troponin complex associates with tropomyosin (Tm1) and controls the contraction of the striated muscle in response to changes in intracellular calcium concentration. The troponin-T subunit isoforms are encoded by a single gene, up. Troponin-T interacts with tropomyosin. (Adapted from FBrf0226138 and PMID:31448287.)
Protein Function (UniProtKB)
Troponin T is the tropomyosin-binding subunit of troponin, the thin filament regulatory complex which confers calcium-sensitivity to striated muscle actomyosin ATPase activity.
(UniProt, P19351)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
int: indented thorax
80-85% of int flies hold wings ventrolaterally, 10% hold them vertically and the remainder maintain normal wing position. In many flies mesonotum indented to variable degree and at various positions; 85% in flies raised at 29 and 45% when raised at 18. More extreme expression in y flies; partially dominant in y genotypes. Fate mapping indicates focus in presumptive thoracic musculature. Indirect flight muscle structure badly deranged, Z-bands disappear as muscles degenerate; also lose a 54k protein. int/int adults flightless and unable to jump; int/+ adults normal.
up: upheld (J.C. Hall)
Wings held upright and mutants unable to jump or fly when homo- or hemizygous. The indirect flight muscles of the thorax are abnormal, with many mitochondria in the muscle fiber envelopes but with defective myofibrils (Hotta and Benzer, 1972; Deak, 1977); electron microscope and electrophoresis studies indicate that these muscles lack internal structure in the Z-bands and Z-band proteins (Fekete and Szidonya, 1979; Mogami et al., 1981). Although wings are held in normal position, wild-type heterozygotes of certain mutant alleles are unable to jump or fly; their muscles contain half the normal amount of Z-band proteins. Fate maps of the behavioral and morphological foci of up and up2 indicate that the gene has its site of action in the presumptive musculature of the ventral mesoderm (Hotta and Benzer, 1972; Deak, 1977). Viability and fertility of up is good. RK1.
Gene Model and Products
Number of Transcripts
18
Number of Unique Polypeptides
15

Please see the JBrowse view of Dmel\up 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 P19351)

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 5.55

Gene model reviewed during 5.42

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Low-frequency RNA-Seq exon junction(s) not annotated.

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.51

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0073851
1525
397
FBtr0073852
1573
389
FBtr0073853
1684
306
FBtr0100561
1456
374
FBtr0100563
1522
396
FBtr0301919
1456
374
FBtr0301920
1525
397
FBtr0301921
1501
389
FBtr0301922
1522
396
FBtr0301923
1570
388
FBtr0308233
1453
373
FBtr0308234
1629
394
FBtr0310136
1597
397
FBtr0310137
1522
396
FBtr0310138
1498
388
FBtr0340617
1546
388
FBtr0340618
1696
388
FBtr0345131
1413
306
Additional Transcript Data and Comments
Reported size (kB)

1.9 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
FBpp0073682
47.4
397
4.31
FBpp0073683
46.6
389
4.30
FBpp0073684
36.5
306
4.30
FBpp0100013
44.8
374
4.36
FBpp0100015
47.3
396
4.31
FBpp0291133
44.9
374
4.37
FBpp0291134
47.5
397
4.31
FBpp0291135
46.7
389
4.31
FBpp0291136
47.4
396
4.32
FBpp0291137
46.5
388
4.32
FBpp0300553
44.8
373
4.37
FBpp0300554
47.2
394
4.62
FBpp0301821
47.5
397
4.32
FBpp0301822
47.4
396
4.31
FBpp0301823
46.5
388
4.30
FBpp0309481
46.5
388
4.30
FBpp0309482
46.5
388
4.30
FBpp0311352
36.5
306
4.30
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

306 aa isoforms: up-PD, up-PT
388 aa isoforms: up-PQ, up-PR, up-PS
Additional Polypeptide Data and Comments
Reported size (kDa)

396, 387, 373 (aa)

Comments
External Data
Post Translational Modification

Some glutamate residues are polyglycylated by TTLL3B. This modification occurs exclusively on glutamate residues and results in polyglycine chains on the gamma-carboxyl group.

(UniProt, P19351)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\up 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).

-0.58

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

up is enriched in border follicle cells relative to follicle cells.

The 1.9 kb up transcript is found in developmental stages where muscles are forming, namely during mid to late embryogenesis, in mid to late pupae, and in adults.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\up 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
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
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 16 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of up
Transgenic constructs containing regulatory region of up
Aberrations (Deficiencies and Duplications) ( 13 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
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
mitochondrion & flight muscle
myosin filament & indirect flight muscle
striated muscle thin filament & indirect flight muscle
Z disc & indirect flight muscle
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (8)
8 of 14
Yes
Yes
8 of 14
Yes
Yes
7 of 14
No
Yes
2  
1 of 14
No
No
1 of 14
No
No
1  
1 of 14
No
No
1 of 14
No
No
1  
1 of 14
No
No
1  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (9)
8 of 14
Yes
Yes
8 of 14
Yes
Yes
8 of 14
Yes
Yes
1 of 14
No
Yes
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
Mus musculus (laboratory mouse) (6)
8 of 14
Yes
Yes
8 of 14
Yes
Yes
8 of 14
Yes
Yes
1  
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (8)
5 of 13
Yes
Yes
3 of 13
No
Yes
2 of 13
No
Yes
2 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Danio rerio (Zebrafish) (21)
7 of 14
Yes
Yes
7 of 14
Yes
Yes
7 of 14
Yes
Yes
6 of 14
No
Yes
6 of 14
No
Yes
5 of 14
No
Yes
5 of 14
No
Yes
5 of 14
No
Yes
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (8)
10 of 14
Yes
Yes
9 of 14
No
Yes
8 of 14
No
Yes
8 of 14
No
Yes
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (2)
11 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
1 of 13
Yes
Yes
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:up. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Drosophila melanogaster (Fruit fly) (1)
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 5 )
Potential Models Based on Orthology ( 7 )
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
Show neighbor-neighbor interactions:
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Other Interaction Browsers

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
RNA-RNA
Physical Interaction
Assay
References
Summary of Genetic Interactions
esyN Network Diagram
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
esyN Network Key:
Suppression
Enhancement
Other Interaction Browsers

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.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
X
Recombination map
1-44
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
12A7-12A7
Limits computationally determined from genome sequence between P{EP}CG1640EP1626 and P{EP}NFATEP1353&P{EP}NFATEP1508
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
12A3-12A3
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Location

1-41.0 +/- 0.5

1-43.5

Left of (cM)
Right of (cM)
Notes

Mapping based on up 'int' alleles.

Stocks and Reagents
Stocks (7)
Genomic Clones (7)
 

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

cDNA Clones (139)
 

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)
RNAi and Array Information
Linkouts
DRSC - Results frm RNAi screens
Antibody Information
Laboratory Generated Antibodies
 

monoclonal

Commercially Available Antibodies
 
Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research
Cell Line Information
Publicly Available Cell Lines
 
    Other Stable Cell Lines
     
      Other Comments

      ChEST reveals this is a target of Mef2.

      The Hrp59 protein binds preferentially to a subset of mRNAs, including up mRNA.

      The genomic organisation of the up locus has been characterised.

      Viability and fertility of up is good.

      Alleles of up show intracistronic non-complementation with the "raised" allele, Act88F8.

      Fate mapping of up mutants suggests their primary site of action is in the presumptive thoracic musculature.

      Electron microscope and electrophoresis studies indicate that these muscles lack internal structure in the Z-bands and Z-band proteins.

      Wings held upright and mutants unable to jump or fly when homo- or hemizygous. The indirect flight muscles of the thorax are abnormal, with many mitochondria in the muscle fiber envelopes but with defective myofibrils; which contain half the normal amount of Z-band proteins.

      Relationship to Other Genes
      Source for database merge of

      Source for merge of: up BcDNA:LD08591

      Additional comments

      Source for merge of up BcDNA:LD08591 was a shared cDNA ( date:030728 ).

      Nomenclature History
      Source for database identify of
      Nomenclature comments
      Etymology
      Synonyms and Secondary IDs (23)
      Reported As
      Symbol Synonym
      BcDNA:LD08591
      Name Synonyms
      Secondary FlyBase IDs
      • FBgn0001267
      • FBgn0003955
      • FBgn0047222
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (0)
      Result
      Result Type
      Title
      External Crossreferences and Linkouts ( 143 )
      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 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.
      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
      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.
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      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
      Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research
      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
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      References (202)