FlyBase Gene Report: Dmel\Snx21

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

Contributions welcome

Other Summaries

Alliance
Auto summary
Interactive Fly

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

JBrowse GBrowse

Help me choose

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (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

enables 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

involved_in 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)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Nucleotide / Polypeptide Records

UniProt

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.

CG3077_1

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\Snx21 in GBrowse 2

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

View exonic expression by developmental stage for Dmel\Snx21

View exonic expression by tissue for Dmel\Snx21

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

FBgn0031457

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0031457

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG3077-RA

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

CG3077

Flygut - An atlas of the Drosophila adult midgut

FBgn0031457

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 )

Disrupted in

Df(2L)Exel6277

(Ryder, 2004.4.26)

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

viable, with Scer\GAL4^Mef2.PR

Snx21^GD10120

viable, with Scer\GAL4^pnr-MD237

Snx21^GD10120

viable, with Scer\GAL4^tin.CΔ4

Snx21^GD10120

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (16)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\SNX21

12 of 15

Yes

Hsap\SNX20

10 of 15

Yes

Hsap\C8orf44-SGK3

1 of 15

Hsap\IFNA6

1 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Hsap\SNX24

1 of 15

Yes

Hsap\SNX25

1 of 15

Hsap\SNX29

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (14)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Snx21

12 of 15

Yes

Mmus\Snx20

10 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Mmus\Snx24

1 of 15

Yes

Mmus\Snx25

1 of 15

Mmus\Snx29

1 of 15

Rattus norvegicus (Norway rat) (14)

Rnor\Snx20

10 of 13

Yes

Rnor\Snx21

7 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Rnor\Snx15

1 of 13

Rnor\Snx16

1 of 13

Rnor\Snx22

1 of 13

Yes

Rnor\Snx24

1 of 13

Yes

Rnor\Snx25

1 of 13

Rnor\Snx29

1 of 13

Xenopus tropicalis (Western clawed frog) (9)

Xtro\snx21

9 of 12

Yes

Xtro\snx20

2 of 12

Yes

Xtro\kif16b

1 of 12

Xtro\snx13

1 of 12

Xtro\snx14

1 of 12

Yes

Xtro\snx15

1 of 12

Xtro\snx16

1 of 12

Xtro\snx22

1 of 12

Yes

Xtro\snx24

1 of 12

Yes

Danio rerio (Zebrafish) (12)

Drer\snx21

12 of 15

Yes

Drer\snx20

9 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Drer\snx24

1 of 15

Yes

Drer\snx25

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (4)

Cele\F13E9.1

1 of 15

Yes

Cele\rskd-1

1 of 15

Yes

Cele\snx-13

1 of 15

Yes

Cele\snx-14

1 of 15

Yes

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\MDM1

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190BNK )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

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 v8.0)

Drosophila melanogaster (Fruit fly) (5)

Gene Symbol

Score

Source

Alignment

1 of 10

1 of 10

1 of 10

1 of 10

snz

1 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 ( 1 )

Allele

Disease

Interaction

References

Snx21^KK101320

exacerbates atypical teratoid rhabdoid tumor

modeled by Snr1^KK101602

(Tegeder et al., 2019)

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?

SNX21; sorting nexin family member 21

12 of 15

SNX20; sorting nexin 20

10 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

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.

FBgn0031457

MIST (protein-protein) - An integrated Molecular Interaction Database

CG3077

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

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)

Bloomington

63610

y¹ v¹; P{TRiP.HMJ30177}attP40

14333

y¹ w^67c23; P{SUPor-P}Snx21^KG08074

VDRC

v109618

P{KK101320}VIE-260B

v25630

w¹¹¹⁸; P{GD10120}v25630/TM3

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 sequenced

BDGP DGC clones

Other clones

DPiM_LD12265

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.

FBgn0031457

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0031457

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

33466

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.

33466

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

FBgn0031457

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

FBgn0031457

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

CG3077_1

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

CG3077

Flygut - An atlas of the Drosophila adult midgut

FBgn0031457

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

33466

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

TC013515

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

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

Dmel_CG3077

modMine - A data warehouse for the modENCODE project

FBgn0031457

Linkouts

DPiM - Drosophila Protein interaction map

FBgn0031457

DroID - A comprehensive database of gene and protein interactions.

FBgn0031457

DRSC - Results frm RNAi screens

FBgn0031457

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0031457

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG3077-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0031457

FlyMine - An integrated database for Drosophila genomics

FBgn0031457

MIST (protein-protein) - An integrated Molecular Interaction Database

CG3077

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG3077

(Tegeder et al., 2019, Zhang et al., 2019, Luck et al., 2014, Friedman et al., 2011, Zhang et al., 2011, Keleman et al., 2009.8.5, Perkins et al., 2009, Eulalio et al., 2007)

DmSNX21

(Koumandou et al., 2011)

Snx21

snx21

(Zhang et al., 2019)

Name Synonyms

Sorting nexin 21

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (30)

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

Report Sections