A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\Bin1

General Information
SymbolDmel\Bin1SpeciesD. melanogaster
NameBicoid interacting protein 1Annotation symbolCG6046
Feature typeprotein_coding_geneFlyBase IDFBgn0024491
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)3RRecombination map
Cytogenetic map89B7-89B7Sequence location3R:12,011,880..12,012,615 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene Bicoid interacting protein 1 is referred to in FlyBase by the symbol Bin1 (CG6046, FBgn0024491). It has the cytological map location 89B7. Its sequence location is 3R:12011880..12012615. Its molecular function is described as: protein binding; transcription corepressor activity. It is involved in the biological processes: negative regulation of transcription, DNA-dependent; negative regulation of transcription from RNA polymerase II promoter. 9 alleles are reported. The phenotypes of these alleles are annotated with 11 unique terms, many of which group under: anatomical structure; adult segment; adult; organ system; organism; adult abdominal segment; cephalopharyngeal skeleton; cuticle; adult mesothoracic segment; peripheral nervous system. It has one annotated transcript and one annotated polypeptide.

External Summaries

hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
89B7-89B7  
Limits computationally determined from genome sequence between P{PZ}blp01618 and P{PZ}gish04895&P{EP}EP3171  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
89B9-89B10
(determined by in situ hybridisation)  
(Wang et al., 2002)
89B-89B
(determined by in situ hybridisation)  
(Zhu et al., 2001)
89B9-89B10
Bin1 is located ~43 kb distal to Sb.  
(Jones, 2000.3.9)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
In direction of increasing cytology: Sb? Bin1?
(Jones, 2000.3.9)
In direction of increasing cytology: Bin1- sra+
(Zhu et al., 2001)
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\Bin1 for information on other features
detailed view FBtr0083254 FBtr0100110 FBtr0083279 FBtr0083255 FBpp0100146 FBpp0082708 FBpp0082731 FBti0058593 FBti0064816 FBti0051895 FBti0052125 FBti0033373 FBti0028861 FBti0016556 FBti0056225 FBti0029337 FBti0100823 FBti0043082 FBti0065480
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
Bin1-RA
FBtr0083279
 NM_079653
  663
  150
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
Bin1-PA  
FBpp0082731  
17.3  
150  
8.48  
  NP_524377
  AAF55284
Additional Polypeptide Data & Comments
Reported size (kD)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Sin3 associated polypeptide p18 (IPR010516)
Histone deacetylase complex, SAP18 subunit (IPR017250)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AE003712
AAF55284
 
AF297546
AAG34996
 
AJ278500
CAB95728
 
AQ254719
 
AY070913
AAL48535
 
BF486394
 
BI163100
 
BI173127
 
BI215449
 
BI240903
 
BP540220
 
BP540221
 
BP550393
 
BP550394
 
BP557503
 
BP557504
 
BP558603
 
BT025229
 
CO191775
 
CO265233
 
CO281629
 
CO294631
 
CO339504
 
CZ487593
 
CZ487594
 
EC198851
 
EC199472
 
EC212954
 
EC215549
 
EC247281
 
EC258729
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (BDGP Project Members, 2000-)
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    deletion
    Bin1[117]
    3R:12,012,159..12,012,759
    comment=Approximate boundaries of the Bin1[117] deletion, resulting from excision of P{EP}sraEP[3462] and reported as removing 601 bases from the P insertion site including 448 of the 633 bases of Bin1.
    evidence=experimental
    (Singh, 2002.3.20, Singh and Hanes, 2004)
    rescue fragment
    Bin1[+t4]
    3R:12,010,186..12,014,206
    comment=position of restriction fragment on reference sequence inferred by FlyBase curator
    evidence=experimental
    linked_to=XbaI-EcoRI_rfrag
    (Singh et al., 2005)
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    •
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data     		Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        hide External Data & Images
        Linkouts
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        BDGP expression data
        •
        Show all BDGP original images, annotations and embryonic microarray data for Bin1
        FlyExpress - Embryonic expression images (BDGP data)
        •
        Show all FlyExpress processed images for Bin1
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        viable
        viable | poor
        lethal | maternal effect
        lethal | conditional - heat sensitive
        lethal | conditional - heat sensitive (with Bin1117)
        lethal | conditional - heat sensitive (with Bin1R7-18)
        lethal | larval stage | recessive | conditional - heat sensitive
        lethal | pupal stage | recessive | conditional - heat sensitive
        Other Phenotypes
        Allele
        visible | dominant
        visible | homeotic (with Df(3R)sbd26), with Scer\GAL4[-]:
        melanotic 'tumor'
        Sterility
        Allele
        male sterile
        female fertile
        Phenotype manifest in
        Allele
        wing
        embryo
        larva
        adult
        adult abdominal segment
        melanotic mass
        abdominal sternite bristle | ectopic (with Df(3R)sbd26), with Scer\GAL4[-]:
        adult abdominal segment 6 (with Df(3R)sbd26), with Scer\GAL4[-]:
        adult abdominal segment 5 | ectopic (with Df(3R)sbd26), with Scer\GAL4[-]:
        embryonic/first instar larval cuticle | anterior | germ-line clone
        cephalopharyngeal skeleton | germ-line clone
        hide Classical Alleles ( 4 )
        For All Classical Alleles Show

        Allele of Bin1ClassMutagenStocksKnown lesion
        Bin1117
          		0 Yes
          Bin1EP34622 Yes
          Bin1R7-18loss of function0 Yes
          Bin1f050051 --
          hide Alleles Carried on Transgenic Constructs ( 5 )
          For All Alleles Carried on Transgenic Constructs Show

          Allele of Bin1ClassMutagenStocksKnown lesion
          Bin1+t40 Yes
          Bin1Act5C.PZ0 Yes
          Bin1GD175150 Yes
          Bin1GD42661 Yes
          Bin1cHa0 Yes
          hide Aneuploid Aberrations
          Useful deficiency
           
          Useful duplication
           
          Disrupted in
          (Singh et al., 2005)
          (Singh et al., 2005)
          (Ryder, 2004.4.26)
          Partially disrupted in
          (Singh et al., 2005)
          hide Transgenic Constructs & Insertions
          Transgenic Constructs
          Type of construct
          Name
          Expression data
          UAS construct
          P{GD17515}
          NA
          P{GD4266}
          NA
          characterization construct
          P{sracHa}
          NA
          Insertions
          Type of insertions
          Name
          Expression data
          miscellaneous insertions
          PBac{WH}Bin1f05005
          NA
          P{?EP}Bin1R7-18
          NA
          P{UASp-YFP.Rab11}sra32
          NA
          insertion of mobile activating element
          P{EP}sraEP3462
          NA
          hide Related Comments
          Please look at the allele reports for the complete phenotype data
          Double heterozygous progeny from crosses using sra and Bin1 mutant alleles are viable and fertile at 22oC and 25oC.
          (Singh et al., 2005)
          hide Gene Ontology: Function, Process & Cellular Component ( 6 )
          hide Molecular Function
          CV term
          Evidence
          References
          protein binding
          inferred from physical interaction with FLYBASE:bcd; FB:FBgn0000166
          (Zhu et al., 2001)
          transcription corepressor activity
          non-traceable author statement
          (Zhu, 2000.8.19)
          hide Biological Process
          CV term
          Evidence
          References
          negative regulation of transcription from RNA polymerase II promoter
          non-traceable author statement
          (Swiss-Prot Project Members, 2000.10.1)
          negative regulation of transcription, DNA-dependent
          inferred from direct assay
          (Zhu et al., 2001)
          hide Cellular Component
          CV term
          Evidence
          References
          Sin3 complex
          inferred from sequence or structural similarity with EMBL:U96915
          (Zhu et al., 2001)
          nucleus
          non-traceable author statement
          (Swiss-Prot Project Members, 2000.10.1)
          hide Sequence Ontology: Class of Gene
          protein_coding_gene
           
          nuclear_gene
           
          hide Interactions & Pathways
          hide Summary of Genetic Interactions
          Interacts with
          Please look at the allele data for full details of the genetic interactions
          Bin1 allele
          Gene
          References
          Bin1R7-18
          bcd
          (Singh et al., 2005)
          unspecified
          Trl
          (Espinas et al., 2000)
          hide External Data
          Linkouts
          BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
          •
          hide Orthologs
          Genome-wide drosophilid orthologs
          Curated drosophilid orthologs
           
          Linkouts
          InParanoid orthologs - Eukaryotic orthologs
          •
          hide Functional Complementation between Species
          hide Inter-Species Misexpression Data
          Produces phenotype in
          Produces NO phenotype in
          hide Stocks & Reagents
          hide Stocks Listed in FlyBase ( 5 )
          Harvard
          -
          PBac{WH}Bin1f05005
          VDRC
          v15710
          w1118; P{GD4266}v15710
          Szeged
          -
          P{EP}sraEP3462 Bin1EP3462
          Bloomington
          17130
          w1118; P{EP}sraEP3462 Bin1EP3462
          9790
          y1 w*; P{UASp-YFP.Rab11}sra32/TM3, Sb1
          hide Genomic Clones ( 1 )
          hide cDNA Clones ( 10 )
          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
          cDNA Clones, End Sequenced (ESTs)
          BDGP DGC clones
          Other clones
          hide RNAi & Array Information
          Affy Oligo
          Linkouts
          DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
          •
          GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
          •
          hide Antibody Information
          hide Other Information
          hide Discoverer
          hide Etymology
          hide Identification
          hide Position Effect Variegation Data
          hide Relationship to Other Genes
          Source for database identity of
          Source for identity of: SAP18 CG6046 Source for merge of: Bin1 BcDNA:RE02417 Source for identity of SAP18 CG6046 was sequence comparison (date:000721). Source for merge of Bin1 BcDNA:RE02417 was a shared cDNA (date:030728).
          (FlyBase, 1996-)
          Source for database merge of
          Additional comments
          Su(var)3-102 mutants show no change in the Bin1 coding region.
          (Zhu et al., 2001)
          hide Comments About Role
          hide Comments About Molecular Function
          hide Other Comments
          Identification: Interacts with bcd protein bound to DNA in a modified yeast two-hybrid screen.
          (Zhu and Hanes, 1998)
          hide External Crossreferences & Linkouts
          Sequence Crossreferences
          RefSeq (Transcripts)
          •
          RefSeq (Proteins)
          •
          DDBJ / EMBL / GenBank
          •
          UniProtKB/Swiss-Prot
          •
          Other Crossreferences
          InterPro domains - A database of protein families, domains, and functional sites
          •
          Sin3 associated polypeptide p18 (IPR010516)
          Histone deacetylase complex, SAP18 subunit (IPR017250)
          Linkouts
          BDGP expression data
          •
          Show all BDGP original images, annotations and embryonic microarray data for Bin1
          BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
          •
          DEDB - Drosophila exon database: splicing graphs
          •
          DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
          •
          FLIGHT - Cell culture data for RNAi and other high-throughput technologies
          •
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          •
          FlyExpress - Embryonic expression images (BDGP data)
          •
          FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
          •
          GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
          •
          GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
          •
          InParanoid orthologs - Eukaryotic orthologs
          •