FlyBase Gene Report: Dmel\Bem46

General Information

Symbol

Dmel\Bem46

Species

D. melanogaster

Name

Bem46

Annotation Symbol

CG18642

Feature Type

protein_coding_gene

FlyBase ID

FBgn0025109

Gene Model Status

Current

Stock Availability

7 publicly available

Enzyme Name (EC)

palmitoyl-protein hydrolase (3.1.2.22)

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

23C4-23C4

Sequence location

2L:2,988,116..2,990,075 [+]

Recombination map

2-8

RefSeq locus

NT_033779 REGION:2988116..2990075

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 (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 palmitoyl-(protein) hydrolase activity

inferred from biological aspect of ancestor with PANTHER:PTN000263918

(GO Reference Genome Project, 2011-)

Biological Process (1 term)

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

is_active_in membrane

inferred from biological aspect of ancestor with PANTHER:PTN000263918

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

PALMITOYL-(PROTEIN) HYDROLASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

palmitoyl-(protein) hydrolase activity

S-hexadecanoyl-L-cysteinyl-[protein] + H2O = L-cysteinyl-[protein] + hexadecanoate + H(+) (3.1.2.22)

RHEA 19233:

Summaries

Gene Group (FlyBase)

PALMITOYL-(PROTEIN) HYDROLASES -: Palmitoyl-(protein) hydrolases are specific for long-chain thioesters of fatty acids and hydrolyze fatty acids from S-acylated cysteine residues in proteins, palmitoyl cysteine and palmitoyl-CoA.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Bem46 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 O76462)

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

Gene model reviewed during 5.40

Gene model reviewed during 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Bem46-RA

FBtr0077643

NM_058024

1710

338

Additional Transcript Data and Comments

Reported size (kB)

1.675 (longest cDNA)

(Ghabrial et al., 1998)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Bem46-PA

FBpp0077328

37.9

338

7.47

O76462

NP_477372

AAF51169

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)

338 (aa)

(Ghabrial et al., 1998)

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\Bem46 using the Feature Mapper tool.

External Data

Crossreferences

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

Bem46_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).

3.54

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

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\Bem46 in JBrowse

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

View exonic expression by developmental stage for Dmel\Bem46

View exonic expression by tissue for Dmel\Bem46

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

FBgn0025109

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

44441/tissue=All

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

FBgn0025109

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0025109

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

FBgn0025109

Flygut - An atlas of the Drosophila adult midgut

FBgn0025109

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Bem46

Stages(s) 1-3
Stages(s) 4-6
Stages(s) 13-16

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 ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Bem46

Transgenic constructs containing regulatory region of Bem46

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2L)Exel7014

(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

Bem46^GD853

viable, with Scer\GAL4^Mef2.PR

Bem46^GD853

viable, with Scer\GAL4^pnr-MD237

Bem46^GD853

viable, with Scer\GAL4^tin.CΔ4

Bem46^GD853

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) (15)

Hsap\ABHD13

14 of 14

Yes

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Yes

Hsap\ACOT2

1 of 14

Yes

Hsap\ACOT4

1 of 14

Yes

Hsap\ACOT6

1 of 14

Yes

Hsap\APEH

1 of 14

Hsap\BAAT

1 of 14

Yes

Hsap\MGLL

1 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) (11)

Rnor\Abhd13

14 of 14

Yes

Rnor\Abhd12b

3 of 14

Yes

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

Rnor\Acot4

1 of 14

Yes

Rnor\Acot5

1 of 14

Yes

Rnor\Acot6

1 of 14

Yes

Rnor\Baat

1 of 14

Yes

Mus musculus (laboratory mouse) (15)

Mmus\Abhd13

14 of 14

Yes

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

Mmus\Acnat2

1 of 14

Yes

Mmus\Acot1

1 of 14

Yes

Mmus\Acot2

1 of 14

Yes

Mmus\Acot3

1 of 14

Yes

Mmus\Acot4

1 of 14

Yes

Mmus\Acot5

1 of 14

Yes

Mmus\Acot6

1 of 14

Yes

Mmus\Baat

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (11)

Xtro\abhd13

7 of 13

Yes

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\pianp

1 of 13

Yes

Xtro\sh3bp5

1 of 13

Danio rerio (Zebrafish) (17)

Drer\abhd13

14 of 14

Yes

Drer\abhd12

3 of 14

Drer\si:ch211-117n7.6

3 of 14

Drer\si:ch211-117n7.7

3 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Yes

Drer\acot16

1 of 14

Yes

Drer\acot17

1 of 14

Yes

Drer\acot18

1 of 14

Yes

Drer\acot19

1 of 14

Yes

Drer\acot20

1 of 14

Yes

Drer\acot21

1 of 14

Yes

Drer\acot22

1 of 14

Yes

Drer\mgll

1 of 14

Yes

Drer\tex30

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (11)

Cele\F01D5.7

4 of 14

Yes

Cele\abhd-12

3 of 14

Cele\F01D5.8

3 of 14

Yes

Cele\Y41E3.18

3 of 14

Cele\Y71G12A.4

3 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

Yes

Cele\T05E7.1

1 of 14

Yes

Cele\W03D8.8

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP008746

12 of 12

Yes

3 of 12

2 of 12

2 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (27)

Atha\WAV2

12 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Yes

Atha\AT3G30380

2 of 13

Atha\AT3G47590

2 of 13

Yes

Atha\AT4G14290

2 of 13

Yes

Atha\AT4G17150

2 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

Yes

Atha\AT1G29840

1 of 13

Yes

Atha\AT1G73480

1 of 13

Yes

Atha\AT1G77420

1 of 13

Yes

Atha\AT2G19550

1 of 13

Yes

Atha\AT2G39400

1 of 13

Yes

Atha\AT2G39420

1 of 13

Yes

Atha\AT3G47560

1 of 13

Yes

Atha\AT3G55180

1 of 13

Yes

Atha\AT5G11650

1 of 13

Yes

Atha\AT5G11910

1 of 13

Yes

Atha\AT5G16120

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\YNL320W

13 of 13

Yes

Scer\YDL057W

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\bem46

12 of 12

Yes

Escherichia coli (enterobacterium) (4)

Ecol\yfhR

9 of 11

Yes

Ecol\frsA

1 of 11

Yes

Ecol\ycjY

1 of 11

Yes

Ecol\yjfP

1 of 11

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Bem46. 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) (3)

CG15111

5 of 13

CG33096

4 of 13

CG1309

3 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?

ABHD13; abhydrolase domain containing 13

14 of 14

621039

ABHD12B; abhydrolase domain containing 12B

3 of 14

ABHD12; abhydrolase domain containing 12, lysophospholipase

3 of 14

613599

POLYNEUROPATHY, HEARING LOSS, ATAXIA, RETINITIS PIGMENTOSA, AND CATARACT; PHARC

PHARC syndrome

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

BioGRID - A database of protein and genetic interactions.

69062

DroID - A comprehensive database of gene and protein interactions.

FBgn0025109

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

2-8

Cytogenetic map

23C4-23C4

Sequence location

2L:2,988,116..2,990,075 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

23C4-23C4

Limits computationally determined from genome sequence between P{PZ}lilli⁰⁰⁶³² and P{PZ}toc⁰¹³⁶¹

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

23C-23C

(Ghabrial, 1998.5.28)

Experimentally Determined Recombination Data

Location

2-8

(FlyBase, 2016)

2-6.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (7)

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

Bloomington

28472

y¹ w^*; P{EP}Bem46^G5989/CyO

NIG-Fly

18642R-1

P{NIG.18642R}1

M2L-0677

y¹ w¹¹¹⁸; Bem46^SK3 P{neoFRT}40A/CyO-Tb

M2L-0678

y¹ w¹¹¹⁸; Bem46^SK8 P{neoFRT}40A/CyO-Tb

2LG-0539

y² VhaAC39-1^cho-1 v¹; P{U6-Bem46.NIG.sgRNA}attP40/CyO

VDRC

v101333

P{KK107625}VIE-260B

v7266

w¹¹¹⁸; P{GD853}v7266/TM3

Genomic Clones (13)

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

cDNA Clones (5)

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.

FBgn0025109

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0025109

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Identified with: SD07645 (BDGP-DGC) <up>FlyBase curator comment: EST subsequently found to be chimeric</up>.

(BDGP Project Members, 2000-)

1.6kb transcription unit identified during molecular analysis of the okr genomic region.

(Ghabrial et al., 1998)

Relationship to Other Genes

Source for database merge of

Source for merge of: Bem46 CG18642

(Bayraktaroglu, 2000.4.8)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (3)

Reported As

Symbol Synonym

Bem46

(National Institute of Genetics Fly Stocks, 2022-, Kumar et al., 2021, Japanese National Institute of Genetics, 2012.5.21, Vázquez et al., 2008, Spellman and Rubin, 2002)

CG18642

(National Institute of Genetics Fly Stocks, 2022-, Keleman et al., 2009.8.5, Spellman and Rubin, 2002)

c1.6

(Ghabrial et al., 1998)

Name Synonyms

Bem46

Secondary FlyBase IDs

FBgn0031486

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 37 )

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.

44441

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.

O76462

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.

O76462

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0025109

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

44441/tissue=All

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

FBgn0025109

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

FBgn0025109

FlyMine - An integrated database for Drosophila genomics

FBgn0025109

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

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

dme:Dmel_CG18642

MARRVEL_MODEL - MARRVEL (model organism gene)

44441

Linkouts

BioGRID - A database of protein and genetic interactions.

69062

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

FBgn0025109

DroID - A comprehensive database of gene and protein interactions.

FBgn0025109

DRSC - Results frm RNAi screens

FBgn0025109

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

Bem46_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0025109

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0025109

Flygut - An atlas of the Drosophila adult midgut

FBgn0025109

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC005853

References (33)

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

3.54

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