FlyBase Gene Report: Dmel\Tmhs

General Information

Symbol

Dmel\Tmhs

Species

D. melanogaster

Name

Tetraspan membrane protein in hair cell stereocilia

Annotation Symbol

CG12026

Feature Type

protein_coding_gene

FlyBase ID

FBgn0262624

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

62B9-62B9

Sequence location

3L:1,885,657..1,891,462 [+]

Recombination map

3-1.0

RefSeq locus

NT_037436 REGION:1885657..1891462

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (2 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in sensory perception of sound

inferred from mutant phenotype

(Cosetti et al., 2008)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in sensory perception of sound

inferred from biological aspect of ancestor with PANTHER:PTN000968268

(GO Reference Genome Project, 2011-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in plasma membrane

inferred from biological aspect of ancestor with PANTHER:PTN000968268

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Lipoma HMGIC fusion partner-like protein

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Tmhs 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 Q9W068)

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

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 5.45

Sequence Ontology: Class of Gene

gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Tmhs-RA

FBtr0072837

NM_139417

1453

265

Tmhs-RB

FBtr0072836

NM_167926

1413

265

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

Tmhs-PA

FBpp0072717

29.8

265

7.62

FBpp0072716

29.8

265

7.62

Q9W068

NP_728691

AAN11506

Polypeptides with Identical Sequences

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

265 aa isoforms: Tmhs-PA, Tmhs-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Lipoma HMGIC fusion partner-like protein

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\Tmhs using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Tmhs_1

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).

0.71

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4 -- 6

dorsal ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)

organism | pair rule expression pattern

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

ventral ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

ventral ectoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

foregut primordium

(Fisher et al., 2012)

inclusive hindgut primordium

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

foregut primordium

(Fisher et al., 2012)

hindgut proper primordium

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\Tmhs in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Tmhs

View exonic expression by tissue for Dmel\Tmhs

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

FBgn0262624

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38251/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262624

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0035289

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262624

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG12026

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 4 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Tmhs

Transgenic constructs containing regulatory region of Tmhs

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

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

partially lethal - majority die, with Scer\GAL4^pnr-MD237

Tmhs^GD15582

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Tmhs^GD442

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

Tmhs^GD442

viable, with Scer\GAL4^tin.CΔ4

Other Phenotypes

Allele

abnormal auditory perception | dominant

Tmhs^P1

abnormal neurophysiology | dominant

Tmhs^P1

some die during pupal stage, with Scer\GAL4^pnr-MD237

Tmhs^GD15582

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (9)

Hsap\LHFPL3

13 of 14

Yes

Hsap\LHFPL4

12 of 14

Yes

Hsap\LHFPL5

11 of 14

Yes

Hsap\LHFPL1

3 of 14

Yes

Hsap\LHFPL6

3 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (9)

Rnor\Lhfpl4

12 of 14

Yes

Rnor\Lhfpl5

11 of 14

Yes

Rnor\Lhfpl1

3 of 14

Yes

Rnor\Lhfpl6

3 of 14

Yes

Rnor\Lhfpl2

2 of 14

Rnor\Tmem211

2 of 14

Rnor\Cldnd1

1 of 14

Yes

Rnor\Lhfpl3

1 of 14

Yes

Rnor\LOC103692025

1 of 14

Yes

Mus musculus (laboratory mouse) (8)

Mmus\Lhfpl4

12 of 14

Yes

Mmus\Lhfpl3

11 of 14

Yes

Mmus\Lhfpl5

11 of 14

Yes

Mmus\Lhfpl1

3 of 14

Yes

Mmus\Lhfp

3 of 14

Yes

Mmus\Lhfpl2

2 of 14

Mmus\Tmem211

2 of 14

Mmus\Cldnd1

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (11)

Xtro\lhfpl3

8 of 13

Yes

Xtro\lhfpl4

6 of 13

Yes

Xtro\fbxl3

5 of 13

Yes

Xtro\lhfpl6

2 of 13

Yes

Xtro\lhfpl1

1 of 13

Yes

Xtro\lhfpl2

1 of 13

Xtro\lhfpl5

1 of 13

Yes

Xtro\LOC100486901

1 of 13

Yes

Xtro\opn1lw

1 of 13

Xtro\tmem47

1 of 13

Xtro\tmem211

1 of 13

Yes

Danio rerio (Zebrafish) (10)

Drer\lhfpl3

13 of 14

Yes

Drer\lhfpl4a

11 of 14

Yes

Drer\lhfpl5a

11 of 14

Yes

Drer\lhfpl4b

10 of 14

Yes

Drer\lhfpl5b

10 of 14

Yes

Drer\lhfpl6

3 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\lhfp-4

13 of 14

Yes

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP005724

12 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

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:Tmhs. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (5)

CG3770

4 of 13

CG14182

1 of 13

kune

1 of 13

pck

1 of 13

sinu

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

deafness, autosomal recessive 67

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

Tmhs^P1

model of autosomal recessive nonsyndromic deafness 67

CEA

(Cosetti et al., 2008)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

LHFPL5; LHFPL tetraspan subfamily member 5

model of autosomal recessive nonsyndromic deafness 67

IEA

(FlyBase, 2019-)

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.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

LHFPL3; LHFPL tetraspan subfamily member 3

13 of 14

609719

LHFPL4; LHFPL tetraspan subfamily member 4

12 of 14

610240

LHFPL5; LHFPL tetraspan subfamily member 5

11 of 14

609427

DEAFNESS, AUTOSOMAL RECESSIVE 67; DFNB67

autosomal recessive nonsyndromic deafness 67

LHFPL1; LHFPL tetraspan subfamily member 1

3 of 14

300566

LHFPL6; LHFPL tetraspan subfamily member 6

3 of 14

606710

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

DroID - A comprehensive database of gene and protein interactions.

FBgn0262624

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-1.0

Cytogenetic map

62B9-62B9

Sequence location

3L:1,885,657..1,891,462 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

62B9-62B9

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-1.0

(FlyBase, 2016)

3-3.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

56345

y¹ w^*; Mi{MIC}Tmhs^MI11577/TM3, Sb¹ Ser¹

10246

mwh¹ P{hsneo}CG2021^neo7 Tmhs^P1 red¹ e¹/TM3, ry^RK Sb¹ Ser¹

NIG-Fly

HMJ21771

y¹ v¹; P{TRiP.HMJ21771}attP40/CyO

VDRC

v102005

P{KK109045}VIE-260B

v43386

w¹¹¹⁸ P{GD15582}v43386

Genomic Clones (23)

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

cDNA Clones (27)

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.

FBgn0262624

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

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Tmhs CG12026

(Cosetti et al., 2008)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG12026

(Rice et al., 2020, Japanese National Institute of Genetics, 2012.5.21, Nelson et al., 2010, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Cosetti et al., 2008)

TMHS

(Cosetti et al., 2008)

Tmhs

(Sutton et al., 2024, Elgart et al., 2016)

Name Synonyms

Tetraspan membrane protein in hair cell stereocilia

Tetraspan membrane protein in hair cell stereocilia ortholog

tetraspan membrane protein in hair cell stereocilia

(Cosetti et al., 2008)

Secondary FlyBase IDs

FBgn0035289
FBgn0002181

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 29 )

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.

38251

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.

Q9W068

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q9W068

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.

Q9W068

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0262624

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38251/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262624

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262624

InterPro - A database of protein families, domains and functional sites

Lipoma HMGIC fusion partner-like protein

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG12026

MARRVEL_MODEL - MARRVEL (model organism gene)

38251

Linkouts

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0262624

DroID - A comprehensive database of gene and protein interactions.

FBgn0262624

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Tmhs_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0035289

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262624

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG12026

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

References (26)

The following external sites may use different assemblies or annotations than FlyBase.

0.71

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