FlyBase Gene Report: Dmel\Snup

General Information

Symbol

Dmel\Snup

Species

D. melanogaster

Name

Snurportin

Annotation Symbol

CG42303

Feature Type

protein_coding_gene

FlyBase ID

FBgn0259199

Gene Model Status

Current

Stock Availability

3 publicly available

Gene Summary

Snurportin (Snup) encodes a transport adaptor protein that functions together with the product of msk to carry out nuclear import of small nuclear RNPs. It binds specifically to the 2,2,7-trimethylguanosine cap structure that is present on mature snRNAs. Snup is an essential gene, and the protein shuttles between the cytoplasm and the nucleus. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

62E8-62E8

Sequence location

3L:2,652,088..2,655,455 [+]

Recombination map

3-3

RefSeq locus

NT_037436 REGION:2652088..2655455

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 (8 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables U1 snRNA binding

inferred from direct assay

(Natalizio and Matera, 2013)

enables U2 snRNA binding

inferred from direct assay

(Natalizio and Matera, 2013)

enables U4 snRNA binding

inferred from direct assay

(Natalizio and Matera, 2013)

Terms Based on Predictions or Assertions (0 terms)

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 snRNA import into nucleus

inferred from electronic annotation with InterPro:IPR017336

(InterPro Project Members, 2004-)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in Cajal body

inferred from direct assay

(Natalizio and Matera, 2013)

located_in cytoplasmic U snRNP body

inferred from direct assay

(Natalizio and Matera, 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from electronic annotation with InterPro:IPR017336

(InterPro Project Members, 2004-)

located_in nucleus

inferred from electronic annotation with InterPro:IPR017336

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the snurportin family. (B7Z0I7)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Protein Function (UniProtKB)

Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs.

(UniProt, B7Z0I7)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Snup 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 B7Z0I7)

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.

Gene model reviewed during 5.46

Gene model reviewed during 5.55

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Snup-RA

FBtr0299683

NM_001144405

3245

351

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

Snup-PA

FBpp0288961

41.5

351

5.16

B7Z0I7

NP_001137877

ACL83233

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Interacts with components of the snRNP complex including SmB and Smn; these interactions are RNA-dependent. Interacts with importin-7 msk but not with importin subunit beta Fs(2)Ket; the interaction is RNA-dependent.

(UniProt, B7Z0I7)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

B7Z0I7

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Snup using the Feature Mapper tool.

External Data

Crossreferences

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

Snup_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).

2.09

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

organism

(Natalizio and Matera, 2013)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in Cajal body

inferred from direct assay

(Natalizio and Matera, 2013)

located_in cytoplasmic U snRNP body

inferred from direct assay

(Natalizio and Matera, 2013)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Snup in JBrowse

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

View exonic expression by developmental stage for Dmel\Snup

View exonic expression by tissue for Dmel\Snup

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

FBgn0259200

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

7354429/tissue=All

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

FBgn0259199

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0259199

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

FBgn0259199

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

CG32297

Flygut - An atlas of the Drosophila adult midgut

FBgn0259199

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

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 Snup

Transgenic constructs containing regulatory region of Snup

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 3 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

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) (1)

Hsap\SNUPN

11 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (1)

Rnor\Snupn

12 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Snupn

12 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\XB990428

6 of 13

Yes

Xtro\snupn

5 of 13

Yes

Xtro\fgf4

1 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\snupn

12 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\F23F1.5

12 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP006658

11 of 12

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\AT4G24880

7 of 13

Yes

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:Snup. 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) (1)

CG42304

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

muscular dystrophy, limb-girdle, autosomal recessive 29

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

Snup^GD10847

model of autosomal recessive limb-girdle muscular dystrophy

CEA

(Iruzubieta et al., 2024)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

SNUPN; snurportin 1

model of autosomal recessive limb-girdle muscular dystrophy type 29

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?

SNUPN; snurportin 1

11 of 14

SNURPORTIN 1; SNUPN

MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 29; LGMDR29

autosomal recessive limb-girdle muscular dystrophy type 29

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

Snup - snRNA:U1:21D

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

Snup - snRNA:U1:82Eb

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

Snup - snRNA:U1:95Ca

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

Snup - snRNA:U1:95Cb

pull down, northern blot, anti tag coimmunoprecipitation

(Natalizio and Matera, 2013)

Snup - snRNA:U1:95Cc

pull down, northern blot, anti tag coimmunoprecipitation

(Natalizio and Matera, 2013)

Snup - snRNA:U2:14B

pull down, northern blot, anti tag coimmunoprecipitation

(Natalizio and Matera, 2013)

Snup - snRNA:U2:34ABa

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

Snup - snRNA:U2:34ABb

pull down, northern blot, anti tag coimmunoprecipitation

(Natalizio and Matera, 2013)

Snup - snRNA:U2:34ABc

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

Snup - snRNA:U2:38ABa

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

Snup - snRNA:U2:38ABb

pull down, northern blot, anti tag coimmunoprecipitation

(Natalizio and Matera, 2013)

Snup - snRNA:U4:25F

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

Snup - snRNA:U4:38AB

pull down, northern blot, anti tag coimmunoprecipitation

(Natalizio and Matera, 2013)

Snup - snRNA:U4:39B

anti tag coimmunoprecipitation, northern blot, pull down

(Natalizio and Matera, 2013)

protein-protein

Physical Interaction

Assay

References

Snup - SmB

anti bait coimmunoprecipitation, western blot

(Natalizio and Matera, 2013)

Snup - Smn

anti bait coimmunoprecipitation, western blot

(Natalizio and Matera, 2013)

Snup - msk

anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation

(Natalizio and Matera, 2013)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

(UniProt, B7Z0I7 )

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0259199

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

7354429

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Nucleocytoplasmic transport

Class of Gene

gene_with_dicistronic_mRNA

(FlyBase Genome Annotators, 2008)

nuclear_gene

(FlyBase Genome Annotators, 2008)

protein_coding_gene

(FlyBase Genome Annotators, 2008)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-3

Cytogenetic map

62E8-62E8

Sequence location

3L:2,652,088..2,655,455 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

62E8-62E8

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-3

(FlyBase, 2016)

3-5.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

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

NIG-Fly

1247R-1

P{NIG.1247R}1

VDRC

v34506

w¹¹¹⁸; P{GD10847}v34506

v40997

w¹¹¹⁸; P{GD10847}v40997

Genomic Clones (8)

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

cDNA Clones (7)

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.

FBgn0259199

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0259199

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Natalizio and Matera, 2013)

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

Annotation CG32297 split into CG42303 and CG42304 in release 5.9 of the genome annotation.

(FlyBase Genome Annotators, 2008)

One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG42303 and CG42304.

(FlyBase Genome Annotators, 2008)

Annotations CG1247 and CG1248 merged as CG32297 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Nomenclature History

Source for database identify of

Source for identity of: Snup CG42303

(Natalizio and Matera, 2013)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG1247

CG32297

(Giot et al., 2003)

CG42303

(Natalizio and Matera, 2013, Japanese National Institute of Genetics, 2012.5.21, FlyBase Genome Annotators, 2008)

Snup

(Natalizio and Matera, 2013)

dSNUP

(Natalizio and Matera, 2013)

Name Synonyms

Snurportin

(Natalizio and Matera, 2013)

Secondary FlyBase IDs

FBgn0035362
FBgn0035363
FBan0032297
FBgn0052297

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 31 )

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.

7354429

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.

ACL83233

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.

B7Z0I7

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

B7Z0I7

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.

B7Z0I7

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0259200

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

7354429/tissue=All

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

FBgn0259199

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

FBgn0259199

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

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

dme:Dmel_CG42303

MARRVEL_MODEL - MARRVEL (model organism gene)

7354429

Linkouts

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

FBgn0259199

DroID - A comprehensive database of gene and protein interactions.

FBgn0259199

DRSC - Results frm RNAi screens

FBgn0259199

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

Snup_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0259199

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0259199

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

CG32297

Flygut - An atlas of the Drosophila adult midgut

FBgn0259199

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

TC003517

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Nucleocytoplasmic transport

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

7354429

References (18)

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

2.09

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