FB2021_01, released Feb 18, 2021

Gene: Dmel\D1

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General Information
Symbol
Dmel\D1
Species
D. melanogaster
Name
D1 chromosomal protein
Annotation Symbol
CG9745
Feature Type
protein_coding_gene
FlyBase ID
FBgn0000412
Gene Model Status
Current
Stock Availability
13 publicly available
Gene Snapshot
D1 chromosomal protein (D1) encodes a multi-AT-hook chromosomal protein that associates with AT-rich satellites, including the SAT-III repeats of the X-chromosome. The product of D1 binds to the minor-groove of the DNA and favors heterochromatin-mediated gene repression involving its interaction with topoisomerase II. [Date last reviewed: 2018-09-06]
Other Summaries
Key Links
Genomic Location
Cytogenetic map
85D1-85D1
Sequence location
3R:9,238,083..9,240,654 [-]
Recombination map

3-48

RefSeq locus
NT_033777 REGION:9238083..9240654
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 (7 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables minor groove of adenine-thymine-rich DNA binding
inferred from direct assay
(Levinger and Varshavsky, 1982)
enables satellite DNA binding
inferred from direct assay
(Blattes et al., 2006)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Alfageme et al., 1980)
located_in heterochromatin
inferred from direct assay
(Swenson et al., 2016)
part_of nucleosome
inferred from direct assay
(Levinger and Varshavsky, 1982, Levinger and Varshavsky, 1982)
located_in nucleus
inferred from direct assay
(Blattes et al., 2006, Alfageme et al., 1980)
located_in polytene chromosome
inferred from direct assay
(Alfageme et al., 1980)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
OTHER DNA BINDING DOMAIN TRANSCRIPTION FACTORS -
The Other DNA binding domain transcription factors group is a collection of DNA-binding transcription factors that do not fit into any of the other major domain-based transcription factor groups.
Protein Function (UniProtKB)
This satellite DNA-associated protein is a double-stranded DNA binding protein specific for tracts of pure at DNA. It may play a role in organizing the higher-order structure of euchromatin as well as heterochromatin.
(UniProt, P22058)
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\D1 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

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

Gene model reviewed during 5.46

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
D1-RA
FBtr0081988
NM_079562
1734
355
D1-RC
FBtr0081987
NM_169262
1811
355
D1-RD
FBtr0301524
NM_169261
1597
355
Additional Transcript Data and Comments
Reported size (kB)

1.734 (compiled cDNA)

(Ashley et al., 1989)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
D1-PA
FBpp0081468
37.0
355
6.57
NP_524286
AAF54341
D1-PC
FBpp0081467
37.0
355
6.57
NP_731320
AAN13412
D1-PD
FBpp0290739
37.0
355
6.57
NP_731319
AAN13411
Polypeptides with Identical Sequences

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

355 aa isoforms: D1-PA, D1-PC, D1-PD
Additional Polypeptide Data and Comments
Reported size (kDa)

355 (aa); 37 (kD)

(Ashley et al., 1989)
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\D1 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
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Alfageme et al., 1980)
located_in heterochromatin
inferred from direct assay
(Swenson et al., 2016)
part_of nucleosome
inferred from direct assay
(Levinger and Varshavsky, 1982, Levinger and Varshavsky, 1982)
located_in nucleus
inferred from direct assay
(Blattes et al., 2006, Alfageme et al., 1980)
located_in polytene chromosome
inferred from direct assay
(Alfageme et al., 1980)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\D1 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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of D1
Transgenic constructs containing regulatory region of D1
Aberrations (Deficiencies and Duplications) ( 5 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (0)
No records found.
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (0)
No records found.
Rattus norvegicus (Norway rat) (0)
No records found.
Xenopus tropicalis (Western clawed frog) (1)
Xtro\ncl
1 of 12
Yes
Yes
Danio rerio (Zebrafish) (0)
No records found.
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
Arabidopsis thaliana (thale-cress) (1)
Atha\HMGA
1 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190DRW )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00010293
Drosophila simulans
Dsim\GD28350
Drosophila sechellia
Dsec\GM26279
Drosophila erecta
Dere\GG17392
Drosophila yakuba
Dyak\GE24795
Drosophila ananassae
Dana\GF18425
Drosophila pseudoobscura pseudoobscura
Dpse\GA22003
Drosophila persimilis
Dper\GL22342
Drosophila willistoni
Dwil\GK14031
Drosophila virilis
Dvir\GJ10103
Drosophila mojavensis
Dmoj\GI22500
Drosophila grimshawi
Dgri\GH15235
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150963 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17026983
Musca domestica
House fly
Mdoa\17015832
Glossina morsitans
Tsetse fly
Gmor\GMOY011909
Glossina morsitans
Tsetse fly
Gmor\GMOY011908
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_05043
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
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?
    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
    D1 - Hr78
    two hybrid array
    (Shokri et al., 2019)
    D1 - Ptx1
    two hybrid array
    (Shokri et al., 2019)
    D1 - Ubx
    bimolecular fluorescence complementation, fluorescence microscopy
    (Bischof et al., 2018)
    D1 - abd-A
    bimolecular fluorescence complementation, fluorescence microscopy
    (Bischof et al., 2018)
    D1 - drm
    two hybrid array
    (Shokri et al., 2019)
    D1 - vnd
    anti tag coimmunoprecipitation, anti tag western blot
    (Zhang et al., 2008)
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement
    View in Interactions Browser
    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
    kay
    enhanceable
    D1
    (Sun et al., 2006)
    lap
    enhanceable
    D1
    (Sun et al., 2006)
    pnr
    enhanceable
    D1
    (Pena-Rangel et al., 2002)
    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
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map

    3-48

    Cytogenetic map
    85D1-85D1
    Sequence location
    3R:9,238,083..9,240,654 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    85D1-85D1
    Limits computationally determined from genome sequence between P{lacW}l(3)L4740L4740 and P{EP}D1EP473
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    85D1-85D2
    (determined by in situ hybridisation)
    (Ashley et al., 1989)
    Experimentally Determined Recombination Data
    Location

    3-48

    (FlyBase, 2016)

    3-46.0

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (13)
    Genomic Clones (17)
     

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

    cDNA Clones (194)
     

    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

    (Jagannathan et al., 2018, Renner et al., 2000)
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of
    Additional comments
    Other Comments

    DNA-protein interactions: genome-wide binding profile assayed for D1 protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).

    (Filion et al., 2010)

    D1 has been isolated and sequenced. The predicted sequence contains a highly basic sequence motif also seen in mammalian and avian proteins that bind α satellite DNA. This motif may be a general feature of proteins that bind AT rich satellite DNA.

    (Ashley et al., 1989)
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 48 )
    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
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    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
    InterPro - A database of protein families, domains and functional sites
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DPiM - Drosophila Protein interaction map
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    Synonyms and Secondary IDs (9)
    Datasets (1)
    Study focus (1)
    Experimental Role
    Project
    Project Type
    Title
    • transgene_used
    FBGSE22069
    Protein profiling reveals five principal chromatin types in Drosophila cells.
    References (96)