FlyBase Gene Report: Dmel\CR33221

General Information

Symbol

Dmel\CR33221

Species

D. melanogaster

Name

Annotation Symbol

CR33221

Feature Type

pseudogene

FlyBase ID

FBgn0053221

Gene Model Status

Current

Stock Availability

3 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

3F2-3F2

Sequence location

X:3,797,497..3,799,028 [-]

Recombination map

1-5

RefSeq locus

NC_004354 REGION:3797497..3799028

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 (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

Please see the JBrowse view of Dmel\CR33221 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

Supported by strand-specific RNA-Seq data.

Gene model reviewed during 5.53

Pseudogene similar to CG33213; retrotransposed (FBrf0207702).

Gene model reviewed during 6.06

Sequence Ontology: Class of Gene

nuclear_gene

(FlyBase Genome Annotators, 2011)

processed_pseudogene

(Hogan and Bettencourt, 2009)

pseudogene

(FlyBase Genome Annotators, 2011, Hogan and Bettencourt, 2009)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

CR33221-RB

FBtr0305348

1532

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

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\CR33221 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).

4.36

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\CR33221 in JBrowse

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

View exonic expression by developmental stage for Dmel\CR33221

View exonic expression by tissue for Dmel\CR33221

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

2768878/tissue=All

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

FBgn0053221

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0053221

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

FBgn0053221

Flygut - An atlas of the Drosophila adult midgut

FBgn0053221

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of CR33221

Transgenic constructs containing regulatory region of CR33221

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:CR33221. 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

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

DroID - A comprehensive database of gene and protein interactions.

FBgn0053221

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-5

Cytogenetic map

3F2-3F2

Sequence location

X:3,797,497..3,799,028 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

3F2-3F2

Limits computationally determined from genome sequence between P{EP}EP1200^EP1200&P{EP}EP1343 and P{EP}CG2930^EP1352 3F1

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-5

(FlyBase, 2016)

1-4.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

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

Bloomington

84071

y¹ v¹; P{TKO.GS05540}attP40

65068

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06026}attP40

Korea

11465

P{EP}CR33221^G11470

Genomic Clones (6)

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

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

IP12731

Other clones

MIP03818

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.

FBgn0053221

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0053221

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Annotation CG33221 renamed CR33221 in release 5.33 of the genome annotation.

(FlyBase Genome Annotators, 2011)

CG33221 is a pseudogene. CG33221 is segregating at least 3 alleles in the Pennsylvanian D. melanogaster populations studied, each harboring one, two, or three copies of a repeat of a 101-amino acid sequence near the N-terminal end. The alleles are also nonfunctional, containing indels within the coding sequence that introduce multiple stop codons. All attempts to amplify CG33221 from cDNA extracted from the the Pennsylvanian D. melanogaster populations studied failed.

(Hogan and Bettencourt, 2009)

Relationship to Other Genes

Source for database merge of

Additional comments

The CR33221 gene may have been derived from the CG33213 gene by retroposition.

(Hogan and Bettencourt, 2009)

The CR33221 and CG33213 genes share at least 50% identity.

(Langille and Clark, 2007)

FlyBase curator comment: The symbol "CG12260" has been used erroneously in FlyBase to name 2 separate annotations (one on chromosome X, the other on arm 3R) in different releases of the genome annotation. The two annotations have been renamed to avoid confusion; they are CG33221 (on the X) and CG33213 (on 3R). CG33213 was labelled "CG12260" in releases 1 and 2, was not annotated in release 3.0 and was labelled "CG33213" in 3.1 of the genome annotation. CG33221 was a new annotation in release 3.1 of the genome annotation, when it was mis-labelled "CG12260".

(FlyBase Genome Annotators, 2004)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (3)

Reported As

Symbol Synonym

CG12260

CG33221

(Chen et al., 2012, Zhang et al., 2010, Hogan and Bettencourt, 2009, Langille and Clark, 2007, Gilfillan et al., 2006)

CR33221

(Transgenic RNAi Project members, 2017-, Schertel et al., 2015, FlyBase Genome Annotators, 2011, Perkins et al., 2009)

Name Synonyms

Secondary FlyBase IDs

FBgn0039556

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 13 )

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.

2768878

Other crossreferences

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

2768878/tissue=All

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

FBgn0053221

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

FBgn0053221

FlyMine - An integrated database for Drosophila genomics

FBgn0053221

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

dme:Dmel_CR33221

MARRVEL_MODEL - MARRVEL (model organism gene)

2768878

Linkouts

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

FBgn0053221

DroID - A comprehensive database of gene and protein interactions.

FBgn0053221

DRSC - Results frm RNAi screens

FBgn0053221

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0053221

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0053221

Flygut - An atlas of the Drosophila adult midgut

FBgn0053221

References (19)

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

4.36

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