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 Snapshot
Nipped-B interacts with Mau2 to form the kollerin complex, which topologically loads the cohesin ring complex onto chromosomes. Nipped-B and cohesin participate in transcriptional regulation and DNA repair. [Date last reviewed: 2016-06-16]
Also Known As
NipB, l(2)02047
Genomic Location
Cytogenetic map
Sequence location
2R:4,691,672..4,729,017 [-]
Recombination map
2-55
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
Belongs to the SCC2/Nipped-B family. (Q7PLI2)
Molecular Function (see GO section for details)
Experimental Evidence
Predictions / Assertions
Summaries
UniProt Contributed Function Data
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)
Gene Model and Products
Number of Transcripts
6
Number of Unique Polypeptides
3

Please see the GBrowse view of Dmel\Nipped-B or 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
Gene Ontology (32 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 (22 terms)
Terms Based on Experimental Evidence (14 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
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 )
inferred from mutant phenotype
Terms Based on Predictions or Assertions (10 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 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 )
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 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 biological aspect of ancestor with PANTHER:PTN000496017
(assigned by GO_Central )
Cellular Component (8 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (6 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 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 biological aspect of ancestor with PANTHER:PTN000496017
(assigned by GO_Central )
inferred from sequence or structural similarity with UniProtKB:Q6KC79
(assigned by UniProt )
Expression Data
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
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 30 )
Transgenic Constructs ( 9 )
Deletions and Duplications ( 44 )
Summary of 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 v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v7.1)
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)
5 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
6 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
11 of 15
Yes
Yes
9 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (5)
7 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)
9 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
9 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900DA )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
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
Human Disease Model Data
FlyBase Human Disease Model Reports
Alleles Reported to Model Human Disease (Disease Ontology)
Download
Models ( 2 )
Allele
Disease
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
Interactions ( 0 )
Allele
Disease
Interaction
References
Comments ( 0 )
 
Human Orthologs (via DIOPT v7.1)
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
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.
InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
Pathways
Gene Group - Pathway Membership (FlyBase)
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
2R:4,691,672..4,729,017 [-]
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 sequences
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 ( 47 )
    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
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    Flygut - An atlas of the Drosophila adult midgut
    FlyMine - An integrated database for Drosophila genomics
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Synonyms and Secondary IDs (9)
    Reported As
    Secondary FlyBase IDs
    • FBan0017704
    • FBgn0010505
    • FBgn0020393
    • FBgn0058281
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (114)