FB2020_01, released Feb 12, 2020

Gene: Dmel\Snx21

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General Information
Symbol
Dmel\Snx21
Species
D. melanogaster
Name
Sorting nexin 21
Annotation Symbol
CG3077
Feature Type
protein_coding_gene
FlyBase ID
FBgn0031457
Gene Model Status
Current
Stock Availability
4 publicly available
Gene Snapshot
Insufficient genetic data for FlyBase to solicit a summary. [Date last reviewed: 2016-06-30]
Other Summaries
Key Links
Genomic Location
Cytogenetic map
23A5-23A5
Sequence location
2L:2,763,416..2,765,665 [-]
Recombination map

2-7

RefSeq locus
NT_033779 REGION:2763416..2765665
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
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
phosphatidylinositol binding
Summaries
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Snx21 or the JBrowse view of Dmel\Snx21 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
Comments on Gene Model

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Snx21-RA
FBtr0077736
NM_134865
1372
326
Snx21-RB
FBtr0335129
NM_001273033
2025
320
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
Snx21-PA
FBpp0077416
37.3
326
6.44
NP_608709
AAF51213
Snx21-PB
FBpp0307128
36.6
320
6.35
NP_001259962
AGB92499
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\Snx21 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (2 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
phosphatidylinositol binding
inferred from electronic annotation with InterPro:IPR001683
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
protein transport
inferred from electronic annotation with InterPro:IPR039937
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Cellular Component (0 terms)
There is no information supporting a Cellular Component term for this gene. (Based on a review of available data on: 2013-12-13 )
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
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\Snx21 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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
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, and Transgenic Constructs
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Snx21
Transgenic constructs containing regulatory region of Snx21
Deletions and Duplications ( 1 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
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\SNX21
12 of 15
Yes
Yes
Hsap\SNX20
9 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
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\Snx21
13 of 15
Yes
Yes
Mmus\Snx20
8 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Snx20
9 of 13
Yes
Yes
Rnor\Snx21
6 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\snx21
8 of 12
Yes
Yes
Xtro\snx20
1 of 12
No
Yes
Danio rerio (Zebrafish) (2)
Drer\snx21
12 of 15
Yes
Yes
Drer\snx20
8 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
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.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190BNK )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\Snx21
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00000606
Drosophila simulans
Dsim\GD22806
Drosophila sechellia
Dsec\GM18201
Drosophila erecta
Dere\GG24494
Drosophila yakuba
Dyak\GE15038
Drosophila ananassae
Dana\GF13873
Drosophila pseudoobscura pseudoobscura
Dpse\GA15910
Drosophila persimilis
Dper\GL26446
Drosophila willistoni
Dwil\GK24480
Drosophila virilis
Dvir\GJ23451
Drosophila mojavensis
Dmoj\GI22902
Drosophila grimshawi
Dgri\GH13141
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091507GY )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17006695
Glossina morsitans
Tsetse fly
Gmor\GMOY006353
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_14327
Mayetiola destructor
Hessian fly
Mdes\Mdes009650
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL010731
Anopheles darlingi
American malaria mosquito
Adar\ADAC007613
Anopheles gambiae
Malaria mosquito
Agam\AGAP009095
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ013306
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0EPU )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA002990
Danaus plexippus
Monarch butterfly
Dple\DPOGS211115-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL012431
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_06273
Tribolium castaneum
Red flour beetle
Tcas\TC013515
Pediculus humanus
Human body louse
Phum\PHUM465010
Rhodnius prolixus
Kissing bug
Rpro\RPRC013864
Cimex lectularius
Bed bug
Clec\CLEC005491
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_10788
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0GSC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR011306
Ixodes scapularis
Black-legged tick
Isca\ISCW019150
Stegodyphus mimosarum
African social velvet spider
Smim\KFM65598.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur23g00400
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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 v7.1 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?
    SNX21; sorting nexin family member 21
    12 of 15
        SNX20; sorting nexin 20
        9 of 15
        613281
            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
            Snx21 - CG3740
            experimental knowledge based
            (Guruharsha et al., 2011)
            Summary of Genetic Interactions
            esyN Network Diagram
            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.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Pathways
            Signaling Pathways (FlyBase)
            Metabolic Pathways
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            2L
            Recombination map

            2-7

            Cytogenetic map
            23A5-23A5
            Sequence location
            2L:2,763,416..2,765,665 [-]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            23A5-23A5
            Limits computationally determined from genome sequence between P{EP}EP832 and P{PZ}oho23B03575
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location

            2-7

            (FlyBase, 2016)

            2-6.2

            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (4)
            Genomic Clones (10)
             

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

            cDNA Clones (19)
             

            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 sequences
            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: Snx21 CG3077

            (Zhang et al., 2019)
            Source for database merge of
            Additional comments
            Other Comments

            dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

            (Kiger et al., 2003)
            Origin and Etymology
            Discoverer
            Etymology
            Identification
            External Crossreferences and Linkouts ( 34 )
            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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
            Other crossreferences
            BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            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
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            modMine - A data warehouse for the modENCODE project
            Linkouts
            DPiM - Drosophila Protein interaction map
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            FLIGHT - Cell culture data for RNAi and other high-throughput technologies
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            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 (5)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            References (29)