FlyBase Gene Report: Dmel\GV1

General Information

Symbol

Dmel\GV1

Species

D. melanogaster

Name

GV1

Annotation Symbol

CG12023

Feature Type

protein_coding_gene

FlyBase ID

FBgn0027790

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

GV1 (GV1) encodes a protein with foci that are observed in interphase nuclei and often associated with nuclear periphery. [Date last reviewed: 2018-09-27] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

62B4-62B6

Sequence location

3L:1,810,588..1,822,903 [+]

Recombination map

3-1.0

RefSeq locus

NT_037436 REGION:1810588..1822903

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (3 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables DNA binding

inferred from direct assay

(De Felice et al., 1999)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

colocalizes_with nuclear membrane

inferred from direct assay

(De Felice et al., 2003)

located_in nucleus

inferred from direct assay

(De Felice et al., 2003)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

GV1 (GV1) encodes a protein with foci that are observed in interphase nuclei and often associated with nuclear periphery. [Date last reviewed: 2018-09-27]

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\GV1 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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9W080)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

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

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

Gene model reviewed during 5.46

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

GV1-RA

FBtr0072784

NM_139408

1196

293

GV1-RB

FBtr0072785

NM_167920

801

180

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

GV1-PA

FBpp0072667

32.2

293

9.91

FBpp0072668

20.1

180

10.10

Q8SXW3

NP_728678

AAN11500

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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\GV1 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

GV1_1

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).

-1.01

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

organism

(De Felice et al., 2003)

Additional Descriptive Data

GV1 transcript is detected in 0-2 h old embryos suggesting that it is maternally deposited. Levels continue to increase throughout development as determined by quantitative RT-PCR assays.

(De Felice et al., 2003)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

organism

• nucleus & nuclear membrane

Comment: interphase

(De Felice et al., 2003)

Additional Descriptive Data

GV1 protein is detected in embryonic cycle 14 interphase nuclei as discrete puncta both internal to and in proximity to the nuclear envelope. Fractionation experiments indicate that a fraction of the nuclear protein is associated with the nuclear envelope/cytoskeleton.

(De Felice et al., 2003)

Marker for

Subcellular Localization

CV Term

Evidence

References

colocalizes_with nuclear membrane

inferred from direct assay

(De Felice et al., 2003)

located_in nucleus

inferred from direct assay

(De Felice et al., 2003)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\GV1 in JBrowse

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

View exonic expression by developmental stage for Dmel\GV1

View exonic expression by tissue for Dmel\GV1

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

FBgn0027790

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38238/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0027790

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0027790

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0027790

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG12023

Flygut - An atlas of the Drosophila adult midgut

FBgn0027790

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 3 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of GV1

Transgenic constructs containing regulatory region of GV1

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)Exel6088

(Ryder, 2004.4.26)

Inferred from location ( 8 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

GV1^GD4827

viable, with Scer\GAL4^Mef2.PR

GV1^GD4827

viable, with Scer\GAL4^pnr-MD237

GV1^GD4827

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) (1)

Agam\AgaP_AGAP006835

6 of 12

Yes

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:GV1. 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

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

BioGRID - A database of protein and genetic interactions.

63767

DroID - A comprehensive database of gene and protein interactions.

FBgn0027790

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-1.0

Cytogenetic map

62B4-62B6

Sequence location

3L:1,810,588..1,822,903 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

62B4-62B6

Limits computationally determined from genome sequence between P{PZ}dlt⁰⁴²⁷⁶ and P{PZ}sls^rL182

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-1.0

(FlyBase, 2016)

3-3.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

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

Bloomington

26030

w¹¹¹⁸; Mi{ET1}GV1^MB05550

37175

y¹ w^*; Mi{MIC}GV1^MI03288

37628

y¹ w^*; Mi{MIC}GV1^MI04306

NIG-Fly

HMJ21452

y¹ v¹; P{TRiP.HMJ21452}attP40/CyO

VDRC

v107768

P{KK110646}VIE-260B

v15397

w¹¹¹⁸ P{GD4827}v15397

Genomic Clones (16)

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

cDNA Clones (40)

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

RH49123

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.

FBgn0027790

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0027790

Antibody Information

Laboratory Generated Antibodies

polyclonal

(De Felice et al., 2003)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Identification: dodeca-satellite binding protein isolated in a yeast one-hybrid assay.

(De Felice et al., 1999)

Relationship to Other Genes

Source for database merge of

Source for merge of: GV1 CG12023

(FlyBase, 1996-)

Source for merge of: CG12023 BcDNA:RH49123

(FlyBase, 1996-)

Additional comments

Source for merge of GV1 CG12023 was sequence comparison ( date:030818 ).

(FlyBase, 1996-)

Source for merge of CG12023 BcDNA:RH49123 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

BcDNA:RH49123

CG12023

(Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Lebo et al., 2009, Giot et al., 2003)

DIP1

(De Felice et al., 2003)

GV1

(Ashwal-Fluss et al., 2014, Napoletano et al., 2011, Lebo et al., 2009, Reiter et al., 2007)

Name Synonyms

GV1

Secondary FlyBase IDs

FBgn0035278
FBgn0061378

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 31 )

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.

38238

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q9W080

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q9W080

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0027790

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38238/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0027790

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0027790

FlyMine - An integrated database for Drosophila genomics

FBgn0027790

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG12023

MARRVEL_MODEL - MARRVEL (model organism gene)

38238

Linkouts

BioGRID - A database of protein and genetic interactions.

63767

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0027790

DroID - A comprehensive database of gene and protein interactions.

FBgn0027790

DRSC - Results frm RNAi screens

FBgn0027790

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

GV1_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0027790

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0027790

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG12023

Flygut - An atlas of the Drosophila adult midgut

FBgn0027790

References (28)

The following external sites may use different assemblies or annotations than FlyBase.

-1.01

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