FB2024_04 , released June 25, 2024
Gene: Dmel\Snp
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General Information
Symbol
Dmel\Snp
Species
D. melanogaster
Name
Snipper
Annotation Symbol
CG44248
Feature Type
protein_coding_gene
FlyBase ID
FBgn0265192
Gene Model Status
Current
Stock Availability
15 publicly available
Enzyme Name (EC)
exodeoxyribonuclease I (3.1.11.1)
exodeoxyribonuclease III (3.1.11.2)
Gene Summary
Snipper (Snp) encodes a non-essential exonuclease in the DnaQ-H family. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
58B1-58B2
Sequence location
Recombination map
2-98
RefSeq locus
NT_033778 REGION:22060950..22069757
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
Gene Ontology (GO) Annotations (6 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
enables 3'-5'-RNA exonuclease activity
inferred from direct assay
(Kupsco et al., 2006)
enables double-stranded DNA 3'-5' DNA exonuclease activity
inferred from direct assay
(Kupsco et al., 2006)
enables single-stranded DNA 3'-5' DNA exonuclease activity
inferred from direct assay
(Kupsco et al., 2006)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables 3'-5'-RNA exonuclease activity
inferred from biological aspect of ancestor with PANTHER:PTN000548991
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR047201
(InterPro Project Members, 2004-)
enables nucleic acid binding
inferred from electronic annotation with InterPro:IPR036397
(InterPro Project Members, 2004-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
NOT involved_in histone mRNA catabolic process
inferred from mutant phenotype
(Kupsco et al., 2006)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
inferred from biological aspect of ancestor with PANTHER:PTN000548991
(GO Reference Genome Project, 2011-)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the ERI2 family. (Q95RQ4)
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
double-stranded DNA 3'-5' DNA exonuclease activity
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates (3.1.11.2)
single-stranded DNA 3'-5' DNA exonuclease activity
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates (3.1.11.1)
Summaries
Gene Snapshot
Snipper (Snp) encodes a non-essential exonuclease in the DnaQ-H family. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
3'-5' DNA EXONUCLEASES -
3'-5'-exodeoxyribonucleases catalyze the sequential degradation of double-stranded DNA acting progressively in a 3'-to-5' direction, releasing nucleoside 5'-phosphates.
3'-5' RNA EXONUCLEASES -
3'-5'-exoribonucleases catalyze the sequential degradation of mononucleotides from a free 3' terminus of an RNA molecule.
Protein Function (UniProtKB)
A broad-specificity exonuclease, capable of degrading both structure-specific DNA and RNA targets without sequence specificity in vitro (PubMed:17135487). Requires two to five unpaired nucleotides in the 3' region for efficient binding and nuclease activity (PubMed:17135487). Binds with higher affinity to RNA and DNA stem-loop substrates compared to single-stranded substrate (PubMed:17135487). Binds to the 3'-end of histone mRNAs and degrades them, suggesting that it might play a role in histone mRNA decay after replication (PubMed:17135487). Can readily cleave the histone stem-loop RNA beyond the -12 (UUU) position in the loop to produce -14 and then -16 oligonucleotide fragments for both the stem-loop and the reverse stem-loop (PubMed:17135487). Cleaves both the single-stranded 3' flank as well as the double-stranded stem portion of histone stem-loop RNA (PubMed:17135487). Might affect histone mRNA 3' processing thereby regulating histone protein expression (PubMed:28626879). Has an important role in development and tissue formation (PubMed:28626879). Might have a role in 5.8S rRNA precursor processing (PubMed:28626879).
(UniProt, Q95RQ4)
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Snp 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 Q95RQ4)

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

Gene model reviewed during 5.49

Shares 5' UTR with upstream gene.

Low-frequency RNA-Seq exon junction(s) not annotated.

Sequence Ontology: Class of Gene
nuclear_gene
(FlyBase Genome Annotators, 2012)
protein_coding_gene
(FlyBase Genome Annotators, 2012)
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Snp-RD
FBtr0339099
NM_137788
1899
281
Snp-RE
FBtr0339100
NM_166502
1578
223
Snp-RF
FBtr0339101
NM_166501
1419
223
Snp-RG
FBtr0339102
NM_166503
1667
223
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
Snp-PD
FBpp0308244
32.1
281
8.26
Q95RQ4
NP_611632
AAM68199
Snp-PE
FBpp0308245
25.7
223
8.26
Q9W2A1
NP_726150
AAF46791
Snp-PF
FBpp0308246
25.7
223
8.26
Q9W2A1
NP_726149
AAM68200
Snp-PG
FBpp0308247
25.7
223
8.26
Q9W2A1
NP_726151
AAM68201
Polypeptides with Identical Sequences

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

223 aa isoforms: Snp-PE, Snp-PF, Snp-PG
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\Snp 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
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).

1.53

Transcript Expression
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
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Snp in JBrowse
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
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
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 9 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Snp
Transgenic constructs containing regulatory region of Snp
Aberrations (Deficiencies and Duplications) ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (3)
Hsap\ERI2
9 of 14
Yes
Yes
Hsap\ERI3
4 of 14
No
Yes
Hsap\ERI1
2 of 14
No
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (4)
Rnor\Eri2
9 of 14
Yes
Yes
Rnor\Eri3
4 of 14
No
Yes
Rnor\Eri1
2 of 14
No
Yes
Rnor\Esrp1
1 of 14
No
No
Mus musculus (laboratory mouse) (4)
Mmus\Eri2
9 of 14
Yes
Yes
Mmus\Eri3
4 of 14
No
Yes
Mmus\Eri1
2 of 14
No
Yes
Mmus\Esrp1
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\eri2
6 of 13
Yes
Yes
Xtro\eri3
3 of 13
No
Yes
Xtro\eri1
1 of 13
No
Yes
Xtro\esrp1
1 of 13
No
No
Danio rerio (Zebrafish) (2)
Drer\eri2
7 of 14
Yes
Yes
Drer\eri1
3 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\M02B7.2
7 of 14
Yes
Yes
Cele\R02D3.8
7 of 14
Yes
Yes
Cele\crn-4
2 of 14
No
Yes
Cele\eri-1
1 of 14
No
Yes
Anopheles gambiae (African malaria mosquito) (0)
Arabidopsis thaliana (thale-cress) (1)
Atha\AT3G15140
7 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\eri1
5 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Snp. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
    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
    SnpGD11912
    exacerbates  tauopathy
    modeled by Hsap\MAPTR406W.UAS
    (Butzlaff et al., 2015)
    SnpGD10043
    exacerbates  tauopathy
    modeled by Hsap\MAPTR406W.UAS
    (Butzlaff et al., 2015)
    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?
    ERI2; ERI1 exoribonuclease family member 2
    9 of 14
        ERI3; ERI1 exoribonuclease family member 3
        4 of 14
        609917
            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
            Other Interaction Browsers
            Summary of Genetic Interactions
            esyN Network Diagram
            Other Interaction Browsers
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            External Data
            Linkouts
            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)
            2R
            Recombination map
            2-98
            Cytogenetic map
            58B1-58B2
            Sequence location
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            58B1-58B2
            Limits computationally determined from genome sequence between P{PZ}l(2)0783707837 and P{EP}CG6393EP2457
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location

            2-98

            (FlyBase, 2016)

            2-103.6

            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (15)
            Genomic Clones (24)
            cDNA Clones (159)
             

            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.

            cDNA Clones, End Sequenced (ESTs)
            BDGP DGC clones
            Other clones
            RNAi and Array Information
            Linkouts
            Antibody Information
            Laboratory Generated Antibodies
             
            Commercially Available Antibodies
             
            Cell Line Information
            Publicly Available Cell Lines
             
              Other Stable Cell Lines
               
                Other Comments

                Area matching Drosophila EST AA441173.

                (Davies, 2001.3.15)
                Relationship to Other Genes
                Source for database merge of

                Source for merge of: CG30327 CG6393

                (FlyBase Genome Annotators, 2008)
                Additional comments

                Annotation CG42257 split into CG44248 (which corresponds to Snp) and CG44249 in release 5.49 of the genome annotation.

                (FlyBase Genome Annotators, 2012)

                Split based in part on on data from FBrf0191914.

                (FlyBase Genome Annotators, 2012)

                Annotations CG30327 and CG6393 merged as CG42257 in release 5.8 of the genome annotation.

                (FlyBase Genome Annotators, 2008)
                Nomenclature History
                Source for database identify of

                Source for identity of: Snp CG42257

                (Kupsco et al., 2006)
                Nomenclature comments
                Etymology

                The gene is named "Snipper" based on its potent exonucleolytic activity in vitro.

                (Kupsco et al., 2006)
                Synonyms and Secondary IDs (7)
                Datasets (0)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                Study result (0)
                Result
                Result Type
                Title
                External Crossreferences and Linkouts ( 44 )
                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
                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
                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
                FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                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)
                Linkouts
                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.
                FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                MIST (protein-protein) - An integrated Molecular Interaction Database
                References (44)