FB2022_03, released June 9, 2022

Gene: Dmel\TM9SF4

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General Information
Symbol
Dmel\TM9SF4
Species
D. melanogaster
Name
Transmembrane 9 superfamily protein member 4
Annotation Symbol
CG7364
Feature Type
protein_coding_gene
FlyBase ID
FBgn0028541
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
Transmembrane 9 superfamily protein member 4 (TM9SF4) encodes a nonaspanin-type protein involved in cellular immunity. [Date last reviewed: 2019-09-12] (FlyBase Gene Snapshot)
All Summaries
Also Known As

BG:DS00797.1 , n(2)k07245

Key Links
Genomic Location
Cytogenetic map
34D1-34D1
Sequence location
Recombination map
2-49
RefSeq locus
NT_033779 REGION:13746952..13773905
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
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
involved_in defense response to Gram-negative bacterium
inferred from mutant phenotype
(Bergeret et al., 2008)
involved_in encapsulation of foreign target
inferred from mutant phenotype
(Bergeret et al., 2008)
involved_in negative regulation of peptidoglycan recognition protein signaling pathway
inferred from mutant phenotype
(Perrin et al., 2015)
involved_in phagocytosis
inferred from mutant phenotype
(Bergeret et al., 2008)
involved_in protein localization to plasma membrane
inferred from mutant phenotype
(Perrin et al., 2015)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in protein localization to membrane
inferred from biological aspect of ancestor with PANTHER:PTN000080197
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in cytoplasmic vesicle
inferred from direct assay
(Perrin et al., 2015)
located_in endomembrane system
inferred from high throughput direct assay
(Tan et al., 2009)
located_in plasma membrane
inferred from direct assay
(Perrin et al., 2015)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in integral component of membrane
inferred from electronic annotation with InterPro:IPR004240
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
is_active_in membrane
inferred from biological aspect of ancestor with PANTHER:PTN000080197
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Transmembrane 9 superfamily protein member 4 (TM9SF4) encodes a nonaspanin-type protein involved in cellular immunity. [Date last reviewed: 2019-09-12]
Gene Group (FlyBase)
NONASPANINS -
Nonaspanins (Transmembrane 9 superfamily) are a family of conserved proteins characterized by a large N-terminal extracellular domain and nine putative transmembrane domains. Nonaspanins are largely uncharacterized, but some members have been implicated in the innate immune response. (Adapted from FBrf0227121, FBrf0232789 and FBrf0206066).
Pathway (FlyBase)
Negative Regulators of Imd Signaling Pathway -
Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\TM9SF4 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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9V3N6)

If you don't see the viewer to the right, 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.

Comments on Gene Model

Shares 5' exon(s) with upstream non-coding gene; shared promoter (one isoform only of this gene; isoform may be male-specific).

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
TM9SF4-RA
FBtr0080532
NM_135825
2461
630
TM9SF4-RB
FBtr0343657
NM_001298978
2669
630
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
TM9SF4-PA
FBpp0080109
72.5
630
8.92
Q9V3N6
NP_609669
AAF53324
TM9SF4-PB
FBpp0310252
72.5
630
8.92
Q9V3N6
NP_001285907
AHN54421
Polypeptides with Identical Sequences

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

630 aa isoforms: TM9SF4-PA, TM9SF4-PB
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\TM9SF4 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
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. 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
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasmic vesicle
inferred from direct assay
(Perrin et al., 2015)
located_in endomembrane system
inferred from high throughput direct assay
(Tan et al., 2009)
located_in plasma membrane
inferred from direct assay
(Perrin et al., 2015)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\TM9SF4 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
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) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 7 )
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 TM9SF4
Transgenic constructs containing regulatory region of TM9SF4
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation ( 2 )
Gene disrupted in
Df(2L)Exel7058
(Ryder, 2004.4.26)
Gene partially disrupted in
Df(2L)mir-968-1002-KO
(Chen et al., 2014)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (4)
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\TM9SF4
14 of 15
Yes
Yes
Hsap\TM9SF2
5 of 15
No
No
Hsap\TM9SF1
2 of 15
No
Yes
Hsap\TM9SF3
2 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (5)
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\Tm9sf4
13 of 15
Yes
Yes
Mmus\Gm364
4 of 15
No
No
Mmus\Tm9sf2
4 of 15
No
No
Mmus\Tm9sf1
2 of 15
No
Yes
Mmus\Tm9sf3
2 of 15
No
No
Rattus norvegicus (Norway rat) (4)
Rnor\Tm9sf4
12 of 13
Yes
Yes
Rnor\Tm9sf2
3 of 13
No
No
Rnor\Tm9sf1
2 of 13
No
Yes
Rnor\Tm9sf3
2 of 13
No
No
Xenopus tropicalis (Western clawed frog) (5)
Xtro\LOC100489507
3 of 12
Yes
No
Xtro\tm9sf2
3 of 12
Yes
No
Xtro\tm9sf1
2 of 12
No
Yes
Xtro\tm9sf3
2 of 12
No
No
Xtro\tm9sf4
2 of 12
No
Yes
Danio rerio (Zebrafish) (5)
Drer\tm9sf4
13 of 15
Yes
Yes
Drer\LOC558202
5 of 15
No
No
Drer\tm9sf2
4 of 15
No
No
Drer\tm9sf1
2 of 15
No
Yes
Drer\tm9sf3
2 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\ZK858.6
12 of 15
Yes
Yes
Cele\tag-123
5 of 15
No
No
Cele\Y41D4A.4
2 of 15
No
No
Arabidopsis thaliana (thale-cress) (12)
Atha\TMN6
9 of 9
Yes
Yes
Atha\TMN7
9 of 9
Yes
Yes
Atha\AT2G24170
8 of 9
No
Yes
Atha\AT5G25100
8 of 9
No
Yes
Atha\EMP1
7 of 9
No
Yes
Atha\AT5G35160
3 of 9
No
Yes
Atha\AT4G12650
2 of 9
No
Yes
Atha\AT1G08350
1 of 9
No
Yes
Atha\AT1G14670
1 of 9
No
Yes
Atha\AT2G01970
1 of 9
No
Yes
Atha\AT5G37310
1 of 9
No
Yes
Atha\TMN1
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (3)
Scer\EMP70
10 of 15
Yes
Yes
Scer\TMN2
10 of 15
Yes
Yes
Scer\TMN3
2 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPBC1105.08
9 of 12
Yes
No
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (2)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
TM9SF2
8 of 10
TM9SF3
4 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 v8.0 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?
    TM9SF4; transmembrane 9 superfamily member 4
    14 of 15
    617727
        TM9SF2; transmembrane 9 superfamily member 2
        5 of 15
        604678
            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
            View in Interactions Browser
            Please see the Physical Interaction reports below for full details
            protein-protein
            Physical Interaction
            Assay
            References
            TM9SF4 - PGRP-LC
            anti tag coimmunoprecipitation, anti tag western blot
            (Perrin et al., 2015)
            Summary of Genetic Interactions
            esyN Network Diagram
            esyN Network Key:
            Suppression
            Enhancement
            View in Interactions Browser
            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
            DCTN1-p150
            enhanceable
            TM9SF4
            (Chang et al., 2013)
            PGRP-LC
            suppressible
            TM9SF4
            (Perrin et al., 2015)
            External Data
            Linkouts
            DroID - A comprehensive database of gene and protein interactions.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Pathways
            Signaling Pathways (FlyBase)
            Negative Regulators of Imd Signaling Pathway -
            Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)
            Metabolic Pathways
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            2L
            Recombination map
            2-49
            Cytogenetic map
            34D1-34D1
            Sequence location
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            34D1-34D1
            Limits computationally determined from genome sequence between P{PZ}kuz03782&P{lacW}kuzk14817 and P{lacW}CG7364k07245
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            34D1-34D2
            (determined by in situ hybridisation)
            (Ashburner et al., 1999, Spradling et al., 1999)
            34D1-34D2
            (BDGP Project Members, 1994-1999)
            Experimentally Determined Recombination Data
            Location

            2-49

            (FlyBase, 2016)

            2-44.9

            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (9)
            Genomic Clones (30)
            cDNA Clones (75)
             

            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 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
            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: BG:DS00797.1 CG7364

            (Guan, 1999.11)

            Source for identity of: TM9SF4 CG7364

            (Bergeret et al., 2008)
            Source for database merge of

            Source for merge of: BG:DS00797.1 CG16861

            (FlyBase, 1996-)
            Additional comments

            Source for merge of BG:DS00797.1 CG16861 was a shared cDNA ( date:010720 ).

            (FlyBase, 1996-)
            Other Comments

            S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.

            (Stroschein-Stevenson et al., 2006)
            Origin and Etymology
            Discoverer
            Etymology
            Identification
            External Crossreferences and Linkouts ( 39 )
            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/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
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            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
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            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
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            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)
            modMine - A data warehouse for the modENCODE project
            Linkouts
            ApoDroso - Functional genomic database for photoreceptor development, survival and function
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            FlyMine - An integrated database for Drosophila genomics
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Synonyms and Secondary IDs (7)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            References (45)