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General Information
Symbol
Dmel\Nipped-B
Species
D. melanogaster
Name
Nipped-B
Annotation Symbol
CG17704
Feature Type
FlyBase ID
FBgn0026401
Gene Model Status
Stock Availability
Gene Summary
Nipped-B (Nipped-B) encodes a protein that interacts with the product of Mau2 to form the kollerin complex, which topologically loads the cohesin ring complex onto chromosomes. The product of Nipped-B and cohesin participate in transcriptional regulation and DNA repair. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
Also Known As

NipB, l(2)02047

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-55
RefSeq locus
NT_033778 REGION:4691672..4729017
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (25 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from physical interaction with FLYBASE:Mau2; FB:FBgn0038300
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000496017
(assigned by GO_Central )
Biological Process (18 terms)
Terms Based on Experimental Evidence (14 terms)
CV Term
Evidence
References
inferred from mutant phenotype
involved_in chromatin looping
inferred from genetic interaction with FLYBASE:ct; FB:FBgn0004198
inferred from mutant phenotype
involved_in learning
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:hh; FB:FBgn0004644
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
(assigned by UniProt )
involved_in short-term memory
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000496017
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000496017
(assigned by GO_Central )
inferred from sequence or structural similarity with UniProtKB:Q6KC79
(assigned by UniProt )
inferred from biological aspect of ancestor with PANTHER:PTN000496017
(assigned by GO_Central )
Cellular Component (5 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000496017
(assigned by GO_Central )
inferred from sequence or structural similarity with UniProtKB:Q6KC79
(assigned by UniProt )
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the SCC2/Nipped-B family. (Q7PLI2)
Summaries
Gene Snapshot
Nipped-B (Nipped-B) encodes a protein that interacts with the product of Mau2 to form the kollerin complex, which topologically loads the cohesin ring complex onto chromosomes. The product of Nipped-B and cohesin participate in transcriptional regulation and DNA repair. [Date last reviewed: 2019-03-14]
Protein Function (UniProtKB)
Plays a structural role in chromatin. Involved in sister chromatid cohesion, probably via an interaction with the cohesin complex. Participates in the transcriptional activation mediated by remote enhancers on genes such as cut and Ubx, possibly by alleviating the cohesin-mediated blocking of enhancer-promoter communication.
(UniProt, Q7PLI2)
Summary (Interactive Fly)

a DNA-binding transcription factor regulates gene expression by controlling cohesin dynamics - regulates of sister chromatid cohesion

Gene Model and Products
Number of Transcripts
6
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\Nipped-B 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

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

Gene model reviewed during 5.47

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0111119
6711
2077
FBtr0111118
6683
2077
FBtr0301454
6604
2053
FBtr0301455
6639
2053
FBtr0301456
6611
2053
FBtr0334994
6273
1957
Additional Transcript Data and Comments
Reported size (kB)

7.0 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0110411
236.7
2077
6.53
FBpp0110410
236.7
2077
6.53
FBpp0290669
233.9
2053
6.42
FBpp0290670
233.9
2053
6.42
FBpp0290671
233.9
2053
6.42
FBpp0307004
223.3
1957
6.45
Polypeptides with Identical Sequences

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

2077 aa isoforms: Nipped-B-PE, Nipped-B-PF
2053 aa isoforms: Nipped-B-PG, Nipped-B-PH, Nipped-B-PI
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\Nipped-B 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
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Nipped-B in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 30 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Nipped-B
Transgenic constructs containing regulatory region of Nipped-B
Aberrations (Deficiencies and Duplications) ( 44 )
Inferred from experimentation ( 44 )
Inferred from location ( 0 )
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    Other Phenotypes
    Allele
    Phenotype manifest in
    Allele
    Orthologs
    Human Orthologs (via DIOPT v8.0)
    Homo sapiens (Human) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    12 of 15
    Yes
    Yes
    Model Organism Orthologs (via DIOPT v8.0)
    Mus musculus (laboratory mouse) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    12 of 15
    Yes
    Yes
    Rattus norvegicus (Norway rat) (1)
    4 of 13
    Yes
    Yes
    Xenopus tropicalis (Western clawed frog) (1)
    7 of 12
    Yes
    Yes
    Danio rerio (Zebrafish) (2)
    11 of 15
    Yes
    Yes
    9 of 15
    No
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (1)
    13 of 15
    Yes
    Yes
    Arabidopsis thaliana (thale-cress) (5)
    6 of 9
    Yes
    Yes
    1 of 9
    No
    Yes
    1 of 9
    No
    Yes
    1 of 9
    No
    Yes
    1 of 9
    No
    Yes
    Saccharomyces cerevisiae (Brewer's yeast) (1)
    10 of 15
    Yes
    Yes
    Schizosaccharomyces pombe (Fission yeast) (1)
    9 of 12
    Yes
    Yes
    Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091900DA )
    Organism
    Common Name
    Gene
    AAA Syntenic Ortholog
    Multiple Dmel Genes in this Orthologous Group
    Drosophila simulans
    Drosophila simulans
    Drosophila sechellia
    Drosophila erecta
    Drosophila yakuba
    Drosophila ananassae
    Drosophila pseudoobscura pseudoobscura
    Drosophila persimilis
    Drosophila willistoni
    Drosophila virilis
    Drosophila mojavensis
    Drosophila grimshawi
    Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500BC )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Musca domestica
    House fly
    Musca domestica
    House fly
    Musca domestica
    House fly
    Musca domestica
    House fly
    Glossina morsitans
    Tsetse fly
    Lucilia cuprina
    Australian sheep blowfly
    Lucilia cuprina
    Australian sheep blowfly
    Mayetiola destructor
    Hessian fly
    Aedes aegypti
    Yellow fever mosquito
    Anopheles darlingi
    American malaria mosquito
    Anopheles gambiae
    Malaria mosquito
    Culex quinquefasciatus
    Southern house mosquito
    Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W008Y )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Bombyx mori
    Silkmoth
    Danaus plexippus
    Monarch butterfly
    Heliconius melpomene
    Postman butterfly
    Apis florea
    Little honeybee
    Apis mellifera
    Western honey bee
    Bombus impatiens
    Common eastern bumble bee
    Bombus terrestris
    Buff-tailed bumblebee
    Linepithema humile
    Argentine ant
    Megachile rotundata
    Alfalfa leafcutting bee
    Nasonia vitripennis
    Parasitic wasp
    Dendroctonus ponderosae
    Mountain pine beetle
    Tribolium castaneum
    Red flour beetle
    Pediculus humanus
    Human body louse
    Rhodnius prolixus
    Kissing bug
    Cimex lectularius
    Bed bug
    Acyrthosiphon pisum
    Pea aphid
    Zootermopsis nevadensis
    Nevada dampwood termite
    Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X008G )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Strigamia maritima
    European centipede
    Ixodes scapularis
    Black-legged tick
    Stegodyphus mimosarum
    African social velvet spider
    Tetranychus urticae
    Two-spotted spider mite
    Daphnia pulex
    Water flea
    Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G00DH )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Ciona intestinalis
    Vase tunicate
    Ciona intestinalis
    Vase tunicate
    Gallus gallus
    Domestic chicken
    Gallus gallus
    Domestic chicken
    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 ( 2 )
    Potential Models Based on Orthology ( 1 )
    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?
    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
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    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
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
    External Data
    Linkouts
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-55
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    41B3-41C1
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    h46-h46
    (determined by in situ hybridisation)
    41C1-41C6
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (6)
    Genomic Clones (23)
    cDNA Clones (141)
     

    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)
      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
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of
      Source for database merge of

      Source for merge of: Nipped-B l(2)02047

      Additional comments

      'Nipped' mutations disrupt one or more of four recessive lethal complementation groups: l(2)41Ae, RpL38, Nipped-A and Nipped-B.

      Other Comments

      Transiently named CG40281 in release 3 of the genome annotation.

      'Nipped' mutations identify four essential complementation groups, l(2)41Ae, RpL38, Nipped-A and Nipped-B, that play distinct roles in regulating ct and N signalling.

      The Nipped-B protein may function architecturally between enhancers and promoters to facilitate enhancer-promoter interactions.

      Nipped-B influences N receptor signalling or N expression primarily during development of the eye. Nipped-B is particularly antagonistic to the insulator activity of Su(H).

      The Nipped-group genes regulate ct and Ubx.

      "G00522; BDGP:Dm0206 ; BDGP:l (2)02047" was stated as revision.

      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 53 )
      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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      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
      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
      Flygut - An atlas of the Drosophila adult midgut
      FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      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
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Synonyms and Secondary IDs (9)
      Reported As
      Symbol Synonym
      Secondary FlyBase IDs
      • FBan0017704
      • FBgn0010505
      • FBgn0020393
      • FBgn0058281
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (131)