FlyBase Gene Report: Dmel\Nbr

General Information

Symbol

Dmel\Nbr

Species

D. melanogaster

Name

Nibbler

Annotation Symbol

CG9247

Feature Type

protein_coding_gene

FlyBase ID

FBgn0032924

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

Possesses 3'-5' exoribonuclease activity. Required for 3'-end trimming of AGO1-bound miRNAs, in particular multiple-isoform miRNAs, which represents a critical step in miRNA maturation. (UniProt, Q9VIF1)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

39A6-39A7

Sequence location

2L:21,160,636..21,163,083 [-]

Recombination map

2-54

RefSeq locus

NT_033779 REGION:21160636..21163083

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 (12 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables 3'-5'-RNA exonuclease activity

inferred from mutant phenotype

(Hayashi et al., 2016, Wang et al., 2016, Han et al., 2011, Liu et al., 2011)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables 3'-5' exonuclease activity

inferred from electronic annotation with InterPro:IPR002562, InterPro:IPR037432

(InterPro Project Members, 2004-)

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR002562, InterPro:IPR036397

(InterPro Project Members, 2004-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

involved_in miRNA processing

inferred from mutant phenotype

(Wang et al., 2016)

involved_in piRNA processing

inferred from mutant phenotype

(Feltzin et al., 2015)

involved_in pre-miRNA 3'-end processing

inferred from mutant phenotype

(Han et al., 2011, Liu et al., 2011)

involved_in primary piRNA processing

inferred from mutant phenotype

(Wang et al., 2016)

involved_in secondary piRNA processing

inferred from mutant phenotype

(Hayashi et al., 2016, Wang et al., 2016)

involved_in transposable element silencing

inferred from mutant phenotype

(Wang et al., 2016)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

is_active_in P granule

inferred from direct assay

(Hayashi et al., 2016)

part_of ribonucleoprotein complex

inferred from direct assay

(Liu et al., 2011)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000341338

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

3'-5' RNA EXONUCLEASES

Protein Family (UniProt)

Belongs to the mut-7 family. (Q9VIF1)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

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)

Possesses 3'-5' exoribonuclease activity. Required for 3'-end trimming of AGO1-bound miRNAs, in particular multiple-isoform miRNAs, which represents a critical step in miRNA maturation.

(UniProt, Q9VIF1)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Nbr 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 Q9VIF1)

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

PDB - An information portal to biological macromolecular structures

7JW6

Comments on Gene Model

Gene model reviewed during 5.52

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Nbr-RA

FBtr0081499

NM_136250

2335

625

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

Nbr-PA

FBpp0081027

72.0

625

7.79

Q9VIF1

NP_610094

AAF53970

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 AGO1; the interaction is not RNA dependent.

(UniProt, Q9VIF1)

Crossreferences

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

PDB - An information portal to biological macromolecular structures

7JW6

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VIF1

Mapped Features

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

External Data

Crossreferences

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

Nbr_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).

-0.13

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood | male -- day 7 of adulthood | male

spermatozoon

(Wasbrough et al., 2010)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

is_active_in P granule

inferred from direct assay

(Hayashi et al., 2016)

part_of ribonucleoprotein complex

inferred from direct assay

(Liu et al., 2011)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Nbr in JBrowse

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

View exonic expression by developmental stage for Dmel\Nbr

View exonic expression by tissue for Dmel\Nbr

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

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

35385/tissue=All

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

FBgn0032924

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0032924

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

FBgn0032924

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

CG9247

Flygut - An atlas of the Drosophila adult midgut

FBgn0032924

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 8 )

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 Nbr

Transgenic constructs containing regulatory region of Nbr

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2L)Exel6047

(Ryder, 2004.4.26)

Inferred from location ( 9 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal

Nbr^f02257

partially lethal - majority die

Nbr^f02257

partially lethal - majority die, with Scer\GAL4^Act5C.PU

Nbr^GD14164

viable

Nbr^EY04057

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Nbr^GD14164

viable, with Scer\GAL4^tin.CΔ4

Nbr^GD14164

viable (with Df(2L)BSC312)

Nbr^f02257

Sterility

Allele

fertile

Nbr^EY04057

fertile (with Df(2L)BSC312)

Nbr^f02257

sterile

Nbr^f02257

Other Phenotypes

Allele

abnormal locomotor behavior | adult stage | progressive (with Df(2L)BSC312)

Nbr^f02257

abnormal neuroanatomy | adult stage | progressive (with Df(2L)BSC312)

Nbr^f02257

melanotic mass phenotype | adult stage, with Scer\GAL4^en.PU

Nbr^RNAi.UAS

melanotic mass phenotype | adult stage, with Scer\GAL4^Tub.PU

Nbr^RNAi.UAS

some die during pupal stage, with Scer\GAL4^Act5C.PU

Nbr^GD14164

visible, with Scer\GAL4^en.PU

Nbr^RNAi.UAS

visible, with Scer\GAL4^Tub.PU

Nbr^RNAi.UAS

visible | progressive (with Df(2L)BSC312)

Nbr^f02257

Phenotype manifest in

Allele

adult brain | progressive (with Df(2L)BSC312)

Nbr^f02257

epithelium | adult stage, with Scer\GAL4^Tub.PU

Nbr^RNAi.UAS

wing | progressive (with Df(2L)BSC312)

Nbr^f02257

wing disc | proximal, with Scer\GAL4^ap.PU

Nbr^UAS.EGFP

wing posterior compartment, with Scer\GAL4^en.PU

Nbr^RNAi.UAS

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) (3)

Hsap\EXD3

13 of 14

Yes

Hsap\EXOSC10

1 of 14

Hsap\WRN

1 of 14

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\Exosc10

1 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Exosc10

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\exd3

7 of 13

Yes

Xtro\exosc10

1 of 13

Xtro\wrn

1 of 13

Danio rerio (Zebrafish) (3)

Drer\exd3

14 of 14

Yes

Drer\exosc10

1 of 14

Drer\LOC101883131

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (5)

Cele\mut-7

13 of 14

Yes

Cele\ZK1098.3

13 of 14

Yes

Cele\Y57A10A.13

4 of 14

Yes

Cele\W04A8.4

1 of 14

Yes

Cele\Y105C5A.1268

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP000530

1 of 12

Yes

Agam\AgaP_AGAP001549

1 of 12

Yes

Agam\AgaP_AGAP002300

1 of 12

Yes

Arabidopsis thaliana (thale-cress) (16)

Atha\AT5G24340

7 of 13

Yes

Atha\AT1G56310

3 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\RRP6

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Nbr. 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) (2)

Exd2

2 of 13

WRNexo

2 of 13

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 ( 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?

EXD3; exonuclease 3'-5' domain containing 3

13 of 14

620859

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

protein-protein

Physical Interaction

Assay

References

Nbr - AGO1

anti tag coimmunoprecipitation, anti tag western blot

(Liu et al., 2011)

Nbr - piwi

anti tag coimmunoprecipitation, western blot, anti tag western blot, peptide massfingerprinting

(Hayashi et al., 2016, Wang et al., 2016)

Summary of Genetic Interactions

Interaction Browsers

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

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

Nbr

(Castillejo-López et al., 2018)

External Data

Subunit Structure (UniProtKB)

Interacts with AGO1; the interaction is not RNA dependent.

(UniProt, Q9VIF1 )

Linkouts

BioGRID - A database of protein and genetic interactions.

61340

DroID - A comprehensive database of gene and protein interactions.

FBgn0032924

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

35385

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-54

Cytogenetic map

39A6-39A7

Sequence location

2L:21,160,636..21,163,083 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

39A6-39A7

Limits computationally determined from genome sequence between P{PZ}l(2)05287⁰⁵²⁸⁷ and P{lacW}l(2)k07215^k07215&P{lacW}snRNA:U4:39B^k09410

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-54

(FlyBase, 2016)

2-54.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

85204

w¹¹¹⁸; PBac{WH}Nbr^f02257/CyO

64001

y¹ v¹; P{TRiP.HMJ30314}attP40

NIG-Fly

HMJ30314

y¹ v¹; P{TRiP.HMJ30314}attP40/CyO

M2L-1065

y¹ w¹¹¹⁸; Nbr^SK1 P{neoFRT}40A/CyO-Tb

M2L-1066

y¹ w¹¹¹⁸; Nbr^SK2 P{neoFRT}40A/CyO-Tb

2LG-0855

y² VhaAC39-1^cho-1 v¹; P{U6-Nbr.NIG.sgRNA}attP40/CyO

VDRC

v52550

w¹¹¹⁸; P{GD14164}v52550

v52612

w¹¹¹⁸; P{GD14164}v52612

Genomic Clones (16)

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

cDNA Clones (93)

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.

FBgn0032924

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0032924

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Castillejo-López et al., 2018, Feltzin et al., 2015)

monoclonal

(Hayashi et al., 2016)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from OSC : Endogenously tagged alleles were established for piwi, shu, Gle1, vir and Nbr in OSC cells.
(Meng et al., 2022)
New stable cell line derived from S2-unspecified : Stable S2 cell lines were generated carrying knockout and/or overexpression allels of AGO1, AGO2 and Nbr.
(Reichholf et al., 2019)

Other Comments

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Nbr CG9247

(Liu et al., 2011)

Nomenclature comments

Etymology

Named 'Nibbler' to reflect its role in 3' shortening of miRNAs.

(Han et al., 2011)

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

Name Synonyms

Nibbler

(Suyama and Kai, 2025, Wang and Lin, 2021, Cacchione et al., 2020, Yamashiro and Siomi, 2018, Hayashi et al., 2016, Hirakata and Siomi, 2016, Wang et al., 2016, Yang et al., 2014)

nibbler

(Castillejo-López et al., 2018, Han et al., 2011, Liu et al., 2011)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 36 )

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.

35385

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.

Q9VIF1

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

Q9VIF1

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.

Q9VIF1

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

35385/tissue=All

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

FBgn0032924

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

FBgn0032924

FlyMine - An integrated database for Drosophila genomics

FBgn0032924

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

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

dme:Dmel_CG9247

MARRVEL_MODEL - MARRVEL (model organism gene)

35385

PDB - An information portal to biological macromolecular structures

7JW6

Linkouts

BioGRID - A database of protein and genetic interactions.

61340

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

FBgn0032924

DroID - A comprehensive database of gene and protein interactions.

FBgn0032924

DRSC - Results frm RNAi screens

FBgn0032924

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

Nbr_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0032924

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0032924

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

CG9247

Flygut - An atlas of the Drosophila adult midgut

FBgn0032924

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

TC032570

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

35385

References (51)

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

-0.13

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