FB2022_02, released March 29, 2022

Gene: Dmel\rngo

Open Close
General Information
Symbol
Dmel\rngo
Species
D. melanogaster
Name
rings lost
Annotation Symbol
CG4420
Feature Type
protein_coding_gene
FlyBase ID
FBgn0030753
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Summary
rings lost (rngo) encodes a ubiquitin receptor that binds to ubiquitinated proteins via its ubiquitin-associated domain. It is an essential protein that is required for proper development of ring canals in the female germ line. [Date last reviewed: 2018-10-04] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
14C6-14C6
Sequence location
Recombination map
1-53
RefSeq locus
NC_004354 REGION:16441433..16445367
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
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables proteasome binding
inferred from physical interaction with FLYBASE:Rpn10; FB:FBgn0015283
(Morawe et al., 2011)
enables ubiquitin binding
inferred from direct assay
(Morawe et al., 2011)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables aspartic-type endopeptidase activity
inferred from electronic annotation with InterPro:IPR001995, InterPro:IPR019103
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in female germline ring canal formation
inferred from mutant phenotype
(Morawe et al., 2011)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in proteolysis
inferred from electronic annotation with InterPro:IPR001995, InterPro:IPR019103
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from high throughput direct assay
(Lee et al., 2014)
inferred from direct assay
(Morawe et al., 2011)
located_in cytosol
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from high throughput direct assay
(Lee et al., 2014)
inferred from direct assay
(Morawe et al., 2011)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
rings lost (rngo) encodes a ubiquitin receptor that binds to ubiquitinated proteins via its ubiquitin-associated domain. It is an essential protein that is required for proper development of ring canals in the female germ line. [Date last reviewed: 2018-10-04]
Gene Group (FlyBase)
A28 ASPARTIC ENDOPEPTIDASES -
A28 aspartic endopeptidases belong to MEROPS family A28. They catalyse the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\rngo 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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VXF9)

If you don't see the viewer to the right, 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.

Comments on Gene Model

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

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
rngo-RA
FBtr0074278
NM_132901
2186
458
rngo-RB
FBtr0343349
NM_001298399
2216
458
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
rngo-PA
FBpp0074054
50.5
458
4.78
NP_573129
AAF48614
rngo-PB
FBpp0310006
50.5
458
4.78
NP_001285328
AHN59798
Polypeptides with Identical Sequences

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

458 aa isoforms: rngo-PA, rngo-PB
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\rngo 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
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)
embryonic stage 7 -- 8
anterior endoderm anlage
(Fisher et al., 2012)
head mesoderm
(Fisher et al., 2012)
hindgut anlage
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior endoderm
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
ventral ectoderm
(Fisher et al., 2012)
embryonic stage 9 -- 10
antennal primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
central brain primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
visual primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
anterior endoderm
(Fisher et al., 2012)
foregut primordium
(Fisher et al., 2012)
head mesoderm
(Fisher et al., 2012)
inclusive hindgut primordium
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior endoderm
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 11 -- 12
anterior midgut primordium
(Fisher et al., 2012)
central brain primordium
(Fisher et al., 2012)
embryonic central brain glial cell
(Fisher et al., 2012)
embryonic central brain neuron
(Fisher et al., 2012)
embryonic neuroblast of ventral nerve cord primordium
(Fisher et al., 2012)
foregut primordium
(Fisher et al., 2012)
hindgut proper primordium
(Fisher et al., 2012)
lateral cord glial cell
(Fisher et al., 2012)
lateral cord neuron
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior midgut primordium
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
embryonic/larval midgut
(Fisher et al., 2012)
embryonic/larval muscle system
(Fisher et al., 2012)
embryonic/larval nervous system
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
larval ventral nerve cord
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
organism | ubiquitous
(Morawe et al., 2011)
larval stage
embryonic/larval brain | ubiquitous
(Morawe et al., 2011)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
day 5 of adulthood & male -- day 7 of adulthood & male
spermatozoon
(Wasbrough et al., 2010)
Additional Descriptive Data

rngo protein is expressed ubiquitously during embryogenesis and in larval and adult tissues.

(Morawe et al., 2011)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from high throughput direct assay
(Lee et al., 2014)
inferred from direct assay
(Morawe et al., 2011)
located_in cytosol
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from high throughput direct assay
(Lee et al., 2014)
inferred from direct assay
(Morawe et al., 2011)
Expression Deduced from Reporters
Reporter: PBac{681.P.FSVS-1}rngoCPTI001324
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult brain cell body rind
(Knowles-Barley, 2011.8.24)
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\rngo 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
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
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 7 )
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 rngo
Transgenic constructs containing regulatory region of rngo
Aberrations (Deficiencies and Duplications) ( 4 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (6)
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\DDI2
14 of 15
Yes
Yes
Hsap\DDI1
13 of 15
No
Yes
Hsap\NRIP2
3 of 15
No
Yes
Hsap\NRIP3
3 of 15
No
Yes
Hsap\RSC1A1
2 of 15
No
Yes
Hsap\UBAC2
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (5)
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\Ddi1
14 of 15
Yes
Yes
Mmus\Ddi2
12 of 15
No
Yes
Mmus\Nrip2
3 of 15
No
Yes
Mmus\Nrip3
3 of 15
No
Yes
Mmus\Ubac2
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (5)
Rnor\Ddi2
9 of 13
Yes
Yes
Rnor\Ddi1
7 of 13
No
Yes
Rnor\Nrip3
3 of 13
No
Yes
Rnor\Nrip2
2 of 13
No
Yes
Rnor\Ubac2
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
Xtro\ddi2
13 of 12
Yes
Yes
Xtro\nrip3
3 of 12
No
Yes
Xtro\ubac2
1 of 12
No
Yes
Danio rerio (Zebrafish) (3)
Drer\ddi2
14 of 15
Yes
Yes
Drer\nrip2
3 of 15
No
Yes
Drer\ubac2
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\ddi-1
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\DDI1
9 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\DDI1
12 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\mud1
9 of 12
Yes
Yes
Spom\SPAC56F8.07
2 of 12
No
Yes
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
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 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?
    DDI2; DNA damage inducible 1 homolog 2
    14 of 15
        DDI1; DNA damage inducible 1 homolog 1
        13 of 15
            NRIP2; nuclear receptor interacting protein 2
            3 of 15
                NRIP3; nuclear receptor interacting protein 3
                3 of 15
                613125
                    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
                    rngo
                    anti tag coimmunoprecipitation, anti tag western blot
                    (Morawe et al., 2011)
                    rngo - Rpn10
                    pull down, anti tag western blot, anti bait coimmunoprecipitation
                    (Morawe et al., 2011)
                    rngo - Ubi-p5E
                    pull down, anti tag western blot, anti bait coimmunoprecipitation
                    (Morawe et al., 2011)
                    rngo - Ubi-p63E
                    pull down, anti tag western blot, anti bait coimmunoprecipitation
                    (Morawe 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
                    BioGRID - A database of protein and genetic interactions.
                    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)
                    X
                    Recombination map
                    1-53
                    Cytogenetic map
                    14C6-14C6
                    Sequence location
                    FlyBase Computed Cytological Location
                    Cytogenetic map
                    Evidence for location
                    14C6-14C6
                    Limits computationally determined from genome sequence between P{EP}EP1547EP1547 and P{EP}CG4928EP1341
                    Experimentally Determined Cytological Location
                    Cytogenetic map
                    Notes
                    References
                    Experimentally Determined Recombination Data
                    Location

                    1-53

                    (FlyBase, 2016)

                    1-54.7

                    (Comeron et al., 2012)
                    Left of (cM)
                    Right of (cM)
                    Notes
                    Stocks and Reagents
                    Stocks (5)
                    Genomic Clones (17)
                     

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

                    cDNA Clones (516)
                     

                    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
                      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
                       

                      polyclonal

                      (Morawe et al., 2011)
                      Commercially Available Antibodies
                       
                      Other Information
                      Relationship to Other Genes
                      Source for database identify of

                      Source for identity of: rngo CG4420

                      (Morawe et al., 2011)
                      Source for database merge of
                      Additional comments
                      Other Comments
                      Origin and Etymology
                      Discoverer
                      Etymology

                      The gene is named "rings lost" after the mutant phenotype (defects in ring canal morphogenesis are seen).

                      (Morawe et al., 2011)
                      Identification
                      External Crossreferences and Linkouts ( 74 )
                      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/TrEMBL - Automatically annotated and unreviewed 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
                      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                      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
                      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                      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
                      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.
                      MARRVEL_MODEL - MARRVEL (model organism gene)
                      modMine - A data warehouse for the modENCODE project
                      Linkouts
                      BioGRID - A database of protein and genetic interactions.
                      DroID - A comprehensive database of gene and protein interactions.
                      DRSC - Results frm RNAi screens
                      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 (8)
                      Study focus (0)
                      Experimental Role
                      Project
                      Project Type
                      Title
                      Study result (8)
                      Result
                      Result Type
                      Title
                      scRNAseq_2020_Cattenoz_NI_seq_clustering
                      Clustering analysis of hemocytes from non-infested third instar larvae
                      scRNAseq_2020_Cattenoz_WI_seq_clustering
                      Clustering analysis of hemocytes from wasp-infested third instar larvae
                      scRNAseq_2020_Cho_NI72LG_seq_clustering
                      Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
                      scRNAseq_2020_Cho_NI96LG_seq_clustering
                      Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
                      scRNAseq_2020_Cho_NI120LG_seq_clustering
                      Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
                      scRNAseq_2020_Cho_WI96LG_seq_clustering
                      Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
                      scRNAseq_2020_Cho_NI96HL_seq_clustering
                      Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
                      scRNAseq_2020_Cho_NI120HL_seq_clustering
                      Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
                      References (48)