FlyBase Gene Report: Dmel\SteXh:CG42398

General Information

Symbol

Dmel\SteXh:CG42398

Species

D. melanogaster

Name

SteXh:CG42398

Annotation Symbol

CG42398

Feature Type

protein_coding_gene

FlyBase ID

FBgn0259817

Gene Model Status

Current

Stock Availability

2 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

Sequence location

211000022279188:1,449..2,180 [+]

Recombination map

RefSeq locus

NW_001845284 REGION:1449..2180

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

NCBI

UCSC

Ensembl

Function

Gene Ontology (GO) Annotations (2 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables protein kinase regulator activity

inferred from electronic annotation with InterPro:IPR000704, InterPro:IPR016149, InterPro:IPR035991

(InterPro Project Members, 2004-)

inferred from sequence orthology with SGD:S000005565

(Gene Ontology Curators, 2002-)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of protein kinase CK2 complex

inferred from sequence orthology with SGD:S000005565

(Gene Ontology Curators, 2002-)

inferred from electronic annotation with InterPro:IPR000704, InterPro:IPR016149, InterPro:IPR035991

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\SteXh:CG42398 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

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Stellate repeat sequence: probable SteXh gene.

Corresponds to repeat annotation RR41752.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

SteXh:CG42398-RA

FBtr0300105

NM_001144069

615

172

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

SteXh:CG42398-PA

FBpp0289382

19.7

172

7.34

B8K3A5

NP_001137541

EED86091

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

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

B8K3A5

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\SteXh:CG42398 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).

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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\SteXh:CG42398 in JBrowse

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

View exonic expression by developmental stage for Dmel\SteXh:CG42398

View exonic expression by tissue for Dmel\SteXh:CG42398

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

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

7354447/tissue=All

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

FBgn0259817

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

FBgn0259817

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 ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of SteXh:CG42398

Transgenic constructs containing regulatory region of SteXh:CG42398

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) (1)

Hsap\CSNK2B

2 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (1)

Rnor\Csnk2b

2 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Csnk2b

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\csnk2b

1 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\csnk2b

2 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\kin-10

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP011438

2 of 12

Yes

Arabidopsis thaliana (thale-cress) (4)

Atha\CKB1

2 of 13

Yes

Atha\CKB2

2 of 13

Yes

Atha\CKB3

2 of 13

Yes

Atha\CKB4

2 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\CKB2

2 of 13

Yes

Scer\CKB1

1 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\ckb1

1 of 12

Yes

Spom\SPBC2G5.02c

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:SteXh:CG42398. 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) (17)

CkIIβ2

3 of 13

CkIIβ

3 of 13

Ssl

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

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

esyN Network Diagram

Other Interaction Browsers

Summary of Genetic Interactions

esyN Network Diagram

Other 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

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Class of Gene

nuclear_gene

(FlyBase Genome Annotators, 2008)

protein_coding_gene

(FlyBase Genome Annotators, 2008)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

211000022279188

Recombination map

Cytogenetic map

Sequence location

211000022279188:1,449..2,180 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

(FlyBase Genome Annotators, 2008)

Left of (cM)

Right of (cM)

Notes

Genetic map position based on localization of SteXh.

(FlyBase Genome Annotators, 2008)

Stocks and Reagents

Stocks (2)

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

Bloomington

63552

y¹ v¹; P{TRiP.HMJ30118}attP40

NIG-Fly

HMJ30118

y¹ v¹; P{TRiP.HMJ30118}attP40/CyO

Genomic Clones (0)

cDNA Clones (2)

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

GM31840

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.

FBgn0259817

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

GM04658

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0259817

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CG42398) in release 5.10 of the genome annotation.

(FlyBase Genome Annotators, 2008)

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 (4)

Reported As

Symbol Synonym

CG42398

(Perkins et al., 2009)

RR41752

(FlyBase Genome Annotators, 2008)

SteXh:CG42398

(FlyBase Genome Annotators, 2008)

StellateXh:CG42398

(Khanna and Fortini, 2015)

Name Synonyms

SteXh:CG42398

(FlyBase Genome Annotators, 2008)

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 ( 19 )

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.

7354447

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.

EED86091

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

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

B8K3A5

Other crossreferences

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

7354447/tissue=All

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

FBgn0259817

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

FBgn0259817

InterPro - A database of protein families, domains and functional sites

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

dme:Dmel_CG42398

MARRVEL_MODEL - MARRVEL (model organism gene)

7354447

Linkouts

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

FBgn0259817

DRSC - Results frm RNAi screens

FBgn0259817

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

References (5)

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

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