FlyBase Gene Report: Dmel\bma

General Information

Symbol

Dmel\bma

Species

D. melanogaster

Name

black match

Annotation Symbol

CG34356

Feature Type

protein_coding_gene

FlyBase ID

FBgn0085385

Gene Model Status

Current

Stock Availability

21 publicly available

Gene Summary

black match (bma) encodes a protein involved in heat sensitivity. [Date last reviewed: 2019-08-01] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

67D1-67D2

Sequence location

3L:9,908,120..9,967,298 [+]

Recombination map

3-32

RefSeq locus

NT_037436 REGION:9908120..9967298

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 (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR000719

(InterPro Project Members, 2004-)

NOT enables protein kinase activity

inferred from sequence or structural similarity with UniProtKB:Q9VAR0

(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 (0 terms)

Gene Group (FlyBase)

SCYL PSEUDOKINASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

black match (bma) encodes a protein involved in heat sensitivity. [Date last reviewed: 2019-08-01]

Gene Group (FlyBase)

SCYL PSEUDOKINASES -: The SCYL family of pseudokinases is found in almost all eukaryotes. Members of this family have been shown to be involved in intracellular trafficking, nuclear tRNA export and chromosome biology. (Adapted from PMID:26981075.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\bma 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 A0A6M3Q8Y2)

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

A non-AUG start codon may be used for translation of one or more transcripts of this gene; based on the presence of conserved protein signatures within the 5' UTR without an in-frame AUG (FBrf0243886).

Gene model reviewed during 5.45

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

Gene model reviewed during 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Stop-codon suppression (UAA) postulated; FBrf0244067.

Gene model reviewed during 6.32

Sequence Ontology: Class of Gene

gene_with_stop_codon_read_through

(FlyBase Genome Annotators, 2020, FlyBase Genome Annotators, 2019-)

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

bma-RD

FBtr0331577

NM_001104100

4175

834

bma-RE

FBtr0331578

NM_001274740

4220

834

bma-RG

FBtr0479873

NM_001382075

5905

864

bma-RH

FBtr0479874

NM_001382076

4170

943

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

bma-PD

FBpp0303967

93.1

834

9.34

FBpp0303968

93.1

834

9.34

FBpp0428206

96.2

864

9.51

C6TP33

AGB94364

bma-PH

FBpp0428207

104.9

943

9.58

QJC18612

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

834 aa isoforms: bma-PD, bma-PE

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

Mapped Features

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

External Data

Crossreferences

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

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).

-0.76

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\bma in JBrowse

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

View exonic expression by developmental stage for Dmel\bma

View exonic expression by tissue for Dmel\bma

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

5740442/tissue=All

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

FBgn0085385

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0085385

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

FBgn0085385

Flygut - An atlas of the Drosophila adult midgut

FBgn0085385

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of bma

Transgenic constructs containing regulatory region of bma

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3L)Exel9048

(Ryder, 2004.4.26)

Gene not disrupted in

Df(3L)vnc^MK

(Wang et al., 2010)

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.

Lethality

Allele

partially lethal - majority die, with Scer\GAL4^pnr-MD237

bma^GD2399

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

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

bma^GD13398

Other Phenotypes

Allele

abnormal body color, with Scer\GAL4^pnr-MD237

bma^GD2399

abnormal heat stress response | third instar larval stage, with Scer\GAL4^ppk.1.9

bma^GD2399

some die during pupal stage, with Scer\GAL4^pnr-MD237

bma^GD2399

visible, with Scer\GAL4^pnr-MD237

bma^GD2399

Phenotype manifest in

Allele

mesothoracic tergum, with Scer\GAL4^pnr-MD237

bma^GD2399

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\SCYL2

3 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\Scyl2

3 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Scyl2

2 of 14

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\scyl2

3 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\scyl2

3 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\ZC581.9

4 of 14

Yes

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP005207

8 of 12

Yes

Agam\AgaP_AGAP002142

2 of 12

Arabidopsis thaliana (thale-cress) (2)

Atha\AT1G22870

4 of 13

Yes

Atha\AT1G71410

4 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\SCY1

6 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\ppk32

5 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:bma. 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)

CG1951

7 of 13

CG1344

2 of 13

yata

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 ( 1 )

Human Ortholog

Disease

Evidence

References

SCYL2; SCY1 like pseudokinase 2

model of arthrogryposis multiplex congenita-4

IEA

(FlyBase, 2019-)

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?

SCYL2; SCY1 like pseudokinase 2

3 of 14

616365

ARTHROGRYPOSIS MULTIPLEX CONGENITA 4, NEUROGENIC, WITH AGENESIS OF THE CORPUS CALLOSUM; AMC4

arthrogryposis multiplex congenita-4

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.

FBgn0085385

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

A8JMD5

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-32

Cytogenetic map

67D1-67D2

Sequence location

3L:9,908,120..9,967,298 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

67D1-67D2

; Limits computationally determined from genome sequence between P{PZ}fry⁰²²⁴⁰ and P{lacW}l(3)L0539^L0539&P{PZ}Dhh1^rL562

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-32

(FlyBase, 2016)

3-24.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (21)

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

Bloomington

73064

w¹¹¹⁸; P{VT028327-p65.AD}attP40

73065

w¹¹¹⁸; P{VT028328-p65.AD}attP40

73066

w¹¹¹⁸; P{VT028340-p65.AD}attP40

72971

w¹¹¹⁸; P{VT028328-GAL4.DBD}attP2

73558

w¹¹¹⁸; P{VT028327-GAL4.DBD}attP2

73559

w¹¹¹⁸; P{VT028340-GAL4.DBD}attP2

25549

w¹¹¹⁸; Mi{ET1}bma^MB07390

Korea

13751

P{VT028340-GAL4}attP2

17525

P{VT028328-GAL4}attP2

VDRC

v109790

P{KK107004}VIE-260B

v203398

P{VT028327-GAL4}attP2

v5199

w¹¹¹⁸; P{GD2399}v5199

More stocks available...

Genomic Clones (29)

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

cDNA Clones (11)

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.

FBgn0085385

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0085385

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG12524 CG14163

(FlyBase Genome Annotators, 2007)

Additional comments

Annotations CG12524 and CG14163 merged as CG34356 in release 5.2 of the genome annotation.

(FlyBase Genome Annotators, 2007)

Nomenclature History

Source for database identify of

Source for identity of: bma CG34356

(Honjo et al., 2016)

Nomenclature comments

Etymology

Named "black match" as tissue-specific RNAi-mediated knock-down causes hypersensitive thermal nociception.

(Honjo et al., 2016)

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG12524

(Foley et al., 2010)

CG14163

(Manning et al., 2002)

CG34356

(Wu et al., 2020, Honjo et al., 2016, Aradska et al., 2015, Hosono et al., 2015, Ashwal-Fluss et al., 2014, Pogson et al., 2014, Ni et al., 2010.12.1, Wang et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, FlyBase Genome Annotators, 2007)

bma

(FlyBase Genome Annotators, 2020, FlyBase Genome Annotators, 2019-, Meltzer et al., 2019, Honjo et al., 2016)

Name Synonyms

CG12524

CG14163

black match

(Honjo et al., 2016)

Secondary FlyBase IDs

FBgn0036061
FBgn0036060

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.

5740442

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.

A0A6M3Q8Y2

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.

A0A6M3Q8Y2

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

5740442/tissue=All

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

FBgn0085385

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

FBgn0085385

FlyMine - An integrated database for Drosophila genomics

FBgn0085385

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

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

dme:Dmel_CG34356

MARRVEL_MODEL - MARRVEL (model organism gene)

5740442

Linkouts

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

FBgn0085385

DroID - A comprehensive database of gene and protein interactions.

FBgn0085385

DRSC - Results frm RNAi screens

FBgn0085385

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0085385

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0085385

Flygut - An atlas of the Drosophila adult midgut

FBgn0085385

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

TC031041

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

A8JMD5

References (47)

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

-0.76

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