FlyBase Gene Report: Dmel\satDNA

General Information

Symbol

Dmel\satDNA

Species

D. melanogaster

Name

satellite DNA

Annotation Symbol

Feature Type

satellite_DNA

FlyBase ID

FBgn0003315

Gene Model Status

Unannotated

Stock Availability

None publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

microsatellite, 1.688, sc1, Prodsat, microsatellites

Function

Gene Ontology (GO) Annotations (0 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

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 (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

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

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Transcript Data

Annotated Transcripts

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Polypeptides with Identical Sequences

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\satDNA using the Feature Mapper tool.

External Data

Crossreferences

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

NA

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\satDNA in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\satDNA

View exonic expression by tissue for Dmel\satDNA

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

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 0 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of satDNA

Transgenic constructs containing regulatory region of satDNA

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:satDNA. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (0)

Human Disease Associations

FlyBase Human Disease Model Reports

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 v9.1 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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

satDNA - Cenp-C

anti tag coimmunoprecipitation, quantitative reverse transcription pcr

(Rošić et al., 2014)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

satellite_DNA

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

Cytogenetic map

Sequence location

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (0)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Genomic Clones (0)

cDNA Clones (0)

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 JBrowse 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

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Transcripts of both strands of 1.688 satDNA repeats have been detected in germinal tissues.

(Usakin et al., 2007)

Satellite DNA from the telomeric region of 2L has silencing properties even when transposed to other regions of the genome.

(Kurenova et al., 1998)

By comparing methylation by Ecol\dam methylase between euchromatic and heterochromatic genes it was determined that the heterochromatic state does not prevent methylase accessibility in vivo.

(Wines et al., 1996)

The distribution of sDBP-X and His1 protein on 1.688-g/cm³ satDNA has been mapped.

(Belikov et al., 1993)

In situ hybridisation experiments performed on a number of cytologically determined rearrangements involving the Y chromosome allows localisation of satellite DNA along the Y chromosome.

(Bonaccorsi and Lohe, 1991)

This is a temporary record designed to include data on Drosophila satellite DNAs.

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (22)

Reported As

Symbol Synonym

1.686

(Torok et al., 2000)

1.688

(Kim et al., 2018, Kuhn et al., 2012, Usakin et al., 2007, Usakin et al., 2006, Xiang and Hawley, 2006, Sun et al., 2003, Leach et al., 2000, Talbert and Henikoff, 2000)

MSs

(Girgis and Sheetlin, 2013)

Prodsat

(Zykova et al., 2021)

SAR-DM

(Yang et al., 2008)

SAT III

(Bobkov et al., 2018, Rošić et al., 2014)

SATI

(Monod et al., 2002)

SATIII

(Monod et al., 2002)

SSR

(Stolle et al., 2013)

SatIII

(Blattes et al., 2006)

microsatellite

(Stolle et al., 2013, Kofler et al., 2008)

satDNA

(Aromolaran et al., 2023, Sproul et al., 2020, Fingerhut et al., 2019, Jagannathan et al., 2019, Hanlon et al., 2018, Satyaki et al., 2014, Hutter, 2009.6.2, Ferree and Barbash, 2008)

satellite

(Chang et al., 2019)

sc1

(Picard, 1992.1.28, Picard, 1992.1.28, Picard, 1992.1.28, Picard, 1992.1.28, Picard, 1992.1.28)

stDNA

(Bashkirov, 2002)

Name Synonyms

359 bp satellites

(Lauria Sneideman and Meller, 2021)

Prodsat

(Lauria Sneideman and Meller, 2021)

microsatellites

(Kim et al., 2014, Girgis and Sheetlin, 2013)

satellite I

(Monod et al., 2002)

satellite III

(Monod et al., 2002)

satellite repeat

(Horn et al., 2004)

satellite repeats

(Lauria Sneideman and Meller, 2021)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 215 )

Sequence Crossreferences

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

References (129)

NA

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