FB2022_02, released March 29, 2022

Gene: Dmel\amx

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General Information
Symbol
Dmel\amx
Species
D. melanogaster
Name
almondex
Annotation Symbol
CG12127
Feature Type
protein_coding_gene
FlyBase ID
FBgn0000077
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Summary
Involved in the control of cell fates in the neurectoderm. Acts as a positive regulator of Notch pathway and is required at different levels during development. (UniProt, Q9U4H5)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
8D2-8D2
Sequence location
Recombination map
1-27
RefSeq locus
NC_004354 REGION:9245915..9247336
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 (6 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
involved_in ectodermal cell fate determination
inferred from mutant phenotype
(assigned by UniProt )
(Michellod et al., 2003)
involved_in lateral inhibition
inferred from mutant phenotype
(Das et al., 2020, Jakobsdottir et al., 2016, Michellod and Randsholt, 2008)
inferred from genetic interaction with FLYBASE:Dl; FB:FBgn0000463
(Michellod et al., 2003)
involved_in mesoderm development
inferred from mutant phenotype
(Corbin et al., 1991)
involved_in neuroblast fate determination
inferred from mutant phenotype
(Michellod et al., 2003, Bodmer et al., 1993)
involved_in positive regulation of Notch signaling pathway
inferred from mutant phenotype
(Salazar et al., 2021, Das et al., 2020, Michellod et al., 2003)
inferred from genetic interaction with FLYBASE:N; FB:FBgn0004647
(Michellod and Randsholt, 2008)
inferred from genetic interaction with FLYBASE:Su(H); FB:FBgn0004837
(Michellod et al., 2003)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in spanning component of plasma membrane
inferred from sequence model
(Jakobsdottir et al., 2016, Michellod and Randsholt, 2008)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
Belongs to the TM2 family. (Q9U4H5)
Protein Signatures (InterPro)
Summaries
Pathway (FlyBase)
Positive Regulators of Notch Signaling Pathway -
The Notch receptor signaling pathway is activated by the binding of the transmembrane receptor Notch (N) to transmembrane ligands, Dl or Ser, presented on adjacent cells. This results in the proteolytic cleavage of N, releasing the intracellular domain (NICD). NICD translocates into the nucleus, interacting with Su(H) and mam to form a transcription complex, which up-regulates transcription of Notch-responsive genes. Positive regulators of the pathway enhance the signal from the sending cell or the response in the receiving cell. (Adapted from FBrf0225731 and FBrf0192604).
Gene Group (FlyBase)
TM2 DOMAIN CONTAINING PROTEINS -
TM2 domain containing (TM2D) proteins are metazoan plasma membrane proteins of unknown function characterized by two highly conserved transmembrane domains connected via a short intracellular loop. They have a short extracellular C-terminal domain and larger, more divergent extracellular N-terminal domain. (Adapted from FBrf0252210.)
Protein Function (UniProtKB)
Involved in the control of cell fates in the neurectoderm. Acts as a positive regulator of Notch pathway and is required at different levels during development.
(UniProt, Q9U4H5)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
amx: almondex
Eyes slightly reduced, narrower below. Trident pattern stronger than in lz. Maternal effect lethal. Studies by Shannon [1972, Genetica (The Hague) 43: 244-56] show that amx progeny and many amx/+ progeny of amx mothers are embryonic lethals. Ovaries and egg production of amx females normal. General disorganization of early embryo with amx/+ progeny of amx mothers less extreme than amx progeny (Shannon, 1973, J. Exp. Zool. 183: 383-400); amx/+ daughters show 0.2% survival; amx/Dp(1;1)lz-2 show considerably higher survival (Campos-Ortega); Lethal embryos exhibit hypertrophy of central nervous system at the expense of epidermal tissue (Lehmann, Dietrich, Jimenez, and Campos-Ortega, 1981, Wilhelm Roux's Arch. Dev. Biol. 190: 226-29; Lehmann, Jimenez, Dietrich, and Campos-Ortega, 1983, Wilhelm Roux's Arch. Dev. Biol. 192: 62-74). Similarly peripheral nervous elements, the sensilla, exhibit increased numbers and abnormal morphology; cells diverted from epidermal to neurological pathway (Hartenstein and Campos-Ortega, 1986, Wilhelm Roux's Arch. Dev. Biol. 195: 210-21). Embryonic phenotype locally rescuable by injections of ooplasm from wild-type or pcx ova during preblastoderm stages (Campos-Ortega, La Bonne and Mahowald, 1985, Dev. Biol. 110: 264-67). lz/amx is wild type. Mosaics in amx/+ daughters of _/_ or amx/+ females show that ventral tissues are sensitive to reduced amx+ activity; no clones of amx tissue found in cuticle of amx/+ daughters of amx mothers (Germeraad and Disano, 1984, Genetics 107: s36). RK2.
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\amx 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 Q9U4H5)

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

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)
amx-RA
FBtr0071331
NM_079905
1422
284
amx-RB
FBtr0307281
NM_001258662
1211
284
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
amx-PA
FBpp0071266
31.4
284
7.73
NP_524644
AAF46474
amx-PB
FBpp0298282
31.4
284
7.73
NP_001245591
AFH07305
Polypeptides with Identical Sequences

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

284 aa isoforms: amx-PA, amx-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\amx 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 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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism
(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

GBrowse - Visual display of RNA-Seq signals

View Dmel\amx 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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 5 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 13 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of amx
Transgenic constructs containing regulatory region of amx
Aberrations (Deficiencies and Duplications) ( 11 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal, with Scer\GAL4Mef2.PR
lethal | neurogenic phenotype
lethal | rescuable maternal effect
lethal - all die before end of pupal stage, with Scer\GAL4pnr-MD237
lethal - all die during embryonic stage | neurogenic phenotype (with Df(1)10-70d)
viable
Sterility
Allele
female sterile
female sterile (with Df(1)Exel9049)
female sterile | recessive
fertile
male fertile
Other Phenotypes
Allele
increased cell number | embryonic stage
neurogenic phenotype | embryonic stage 8 | maternal effect
neurogenic phenotype | embryonic stage | maternal effect
neurogenic phenotype | embryonic stage | maternal effect (with Df(1)BSC663)
some die during embryonic stage | neurogenic phenotype (with Df(1)10-70d)
some die during pupal stage, with Scer\GAL4pnr-MD237
visible | recessive
Phenotype manifest in
Allele
ectoderm
embryonic/larval neuron | embryonic stage | maternal effect | increased number (with Df(1)Exel9049)
embryonic epidermis
epidermis
epidermis (with Df(1)10-70d)
epidermis | rescuable maternal effect
external sensory organ precursor cell | embryonic stage
eye
nervous system
nervous system (with Df(1)10-70d)
nervous system | rescuable maternal effect
neuroblast | embryonic stage 8 | maternal effect | increased number
ommatidium
sensory mother cell
thorax
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
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\TM2D3
12 of 15
Yes
Yes
 
3  
Hsap\TM2D1
2 of 15
No
No
Hsap\TM2D2
1 of 15
No
No
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
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\Tm2d3
12 of 15
Yes
Yes
Mmus\Tm2d1
2 of 15
No
No
Mmus\Tm2d2
1 of 15
No
No
Rattus norvegicus (Norway rat) (3)
Rnor\Tm2d3
4 of 13
Yes
Yes
Rnor\Tm2d1
1 of 13
No
No
Rnor\Tm2d2
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\tm2d3
12 of 12
Yes
Yes
Xtro\tm2d2
1 of 12
No
No
Danio rerio (Zebrafish) (3)
Drer\tm2d3
12 of 15
Yes
Yes
Drer\tm2d1
1 of 15
No
No
Drer\tm2d2
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\C41D11.9
13 of 15
Yes
Yes
Cele\Y66D12A.21
2 of 15
No
No
Cele\C02F5.13
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.
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
bisc
4 of 10
amrt
3 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 ( 2 )
Allele
Disease
Interaction
References
amxf06362
ameliorates  neurofibromatosis
modeled by Nf1E2
(Walker et al., 2013)
amxGD1168
ameliorates  neurofibromatosis
modeled by Nf1E2
(Walker et al., 2013)
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?
TM2D3; TM2 domain containing 3
12 of 15
610014
       
      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.
      Dmel gene
      Ortholog showing functional complementation
      Supporting References
      amx
      Hsap\TM2D3
      (Jakobsdottir et al., 2016)
      Interactions
      Summary of Physical Interactions
      esyN Network Diagram
      Interactions Browser
      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
      amx
      suppressible
      N
      (Michellod and Randsholt, 2008)
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Nf1
      suppressible
      amx
      (Walker et al., 2013)
      External Data
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      Pathways
      Signaling Pathways (FlyBase)
      Positive Regulators of Notch Signaling Pathway -
      The Notch receptor signaling pathway is activated by the binding of the transmembrane receptor Notch (N) to transmembrane ligands, Dl or Ser, presented on adjacent cells. This results in the proteolytic cleavage of N, releasing the intracellular domain (NICD). NICD translocates into the nucleus, interacting with Su(H) and mam to form a transcription complex, which up-regulates transcription of Notch-responsive genes. Positive regulators of the pathway enhance the signal from the sending cell or the response in the receiving cell. (Adapted from FBrf0225731 and FBrf0192604).
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map
      1-27
      Cytogenetic map
      8D2-8D2
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      8D2-8D2
      Limits computationally determined from genome sequence between P{EP}EP1450&P{EP}EP1356 and P{EP}EP912EP912
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      8D4-8D9
      (Michellod, 1999.12.20)
      8D4-8E2
      (Green and Green, 1956)
      Experimentally Determined Recombination Data
      Location

      1-27

      (FlyBase, 2016)

      1-28.4

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (8)
      Genomic Clones (9)
       

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

      cDNA Clones (23)
       

      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 database merge of

        Source for merge of: amx BcDNA:GH02974

        (FlyBase, 1996-)
        Additional comments

        Source for merge of amx BcDNA:GH02974 was sequence comparison ( date:000519 ).

        (FlyBase, 1996-)
        Other Comments

        amx is a neurogenic gene required initially to ensure the correct number of PNS precursors. amx is not required for the late epidermal maintenance function.

        (Bodmer et al., 1993)

        amx is needed for proper mesoderm differentiation prior to the onset of nau expression.

        (Corbin et al., 1991)

        Mutant alleles cause hypertrophy in nau expressing cells.

        (Corbin et al., 1991)

        Ecol\lacZ reporter gene constructs demonstrate that amx is required to restrict the number of competent cells that will become sensory mother cells, SMCs.

        (Goriely et al., 1991)

        Increasing the number of wild type copies of amx does not modify the bib mutant phenotype.

        (de la Concha et al., 1988)

        Normal amx function is required during zygotic development for the normal development of the eye and during oogenesis for the synthesis of a maternal component required for neurogenesis and mesoderm diffentiation.

        Origin and Etymology
        Discoverer

        Ball, 20th Nov. 1932.

        Etymology
        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/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
        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
        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
        Synonyms and Secondary IDs (5)
        Datasets (8)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (8)
        Result
        Result Type
        Title
        scRNAseq_2020_Cattenoz_NI_seq_clustering
        Clustering analysis of hemocytes from non-infested third instar larvae
        scRNAseq_2020_Cattenoz_WI_seq_clustering
        Clustering analysis of hemocytes from wasp-infested third instar larvae
        scRNAseq_2020_Cho_NI72LG_seq_clustering
        Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
        scRNAseq_2020_Cho_NI96LG_seq_clustering
        Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
        scRNAseq_2020_Cho_NI120LG_seq_clustering
        Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
        scRNAseq_2020_Cho_WI96LG_seq_clustering
        Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
        scRNAseq_2020_Cho_NI96HL_seq_clustering
        Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
        scRNAseq_2020_Cho_NI120HL_seq_clustering
        Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
        References (63)