FlyBase Gene Report: Dmel\sba

General Information

Symbol

Dmel\sba

Species

D. melanogaster

Name

six-banded

Annotation Symbol

CG13598

Feature Type

protein_coding_gene

FlyBase ID

FBgn0016754

Gene Model Status

Current

Stock Availability

29 publicly available

Gene Summary

Non-catalytic component of the polycomb repressive deubiquitinase (PR-DUB) complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-119' (H2AK118ub1) (PubMed:36180891). Important for maintaining stability of the PR-DUB complex (PubMed:36180891). Probable epigenetic regulator involved in developmental pattern formation and eye development (PubMed:22726846, PubMed:9372180). (UniProt, A8JR92)

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All Summaries

Alliance
Auto summary
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

95C9-95C12

Sequence location

3R:23,894,174..23,922,973 [-]

Recombination map

3-81

RefSeq locus

NT_033777 REGION:23894174..23922973

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 (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables chromatin binding

inferred from sequence or structural similarity with UniProtKB:Q9P267

(Gene Ontology Curators, 2002-)

enables DNA binding

inferred from electronic annotation with InterPro:IPR001739, InterPro:IPR016177

(InterPro Project Members, 2004-)

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

located_in nucleus

inferred from sequence or structural similarity with UniProtKB:Q9P267

(Gene Ontology Curators, 2002-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Protein Function (UniProtKB)

(UniProt, A8JR92)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\sba 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 A8JR92)

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

Stop-codon suppression (UGA) postulated; FBrf0216884.

Gene model reviewed during 5.39

Apparent introns within first coding exon in cDNAs described in X98235 and AY058767 (SD04244) are likely to be artifacts; possibly caused by reverse transcriptase template-switching in regions of CAG repeats.

Gene model reviewed during 5.44

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

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

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

sba-RC

FBtr0112888

NM_001104422

6427

1385

sba-RD

FBtr0112889

NM_001104423

5902

1583

sba-RE

FBtr0308562

NM_176549

5710

1583

sba-RF

FBtr0308563

NM_001260342

5431

1426

sba-RG

FBtr0308564

NM_170094

5523

1362

sba-RH

FBtr0330380

NM_001275959

5902

1606

sba-RI

FBtr0335206

NM_001275960

5573

1291

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

sba-PC

FBpp0111801

148.4

1385

10.61

FBpp0111802

168.6

1583

10.81

FBpp0300786

168.6

1583

10.81

FBpp0300787

151.4

1426

10.77

FBpp0300788

145.8

1362

10.63

FBpp0303406

170.9

1606

10.80

FBpp0307193

138.1

1291

10.56

A0A0B4KHQ9

NP_001262889

AGB96269

Polypeptides with Identical Sequences

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

1583 aa isoforms: sba-PD, sba-PE

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Component of the polycomb repressive deubiquitinase (PR-DUB) complex, at least composed of caly/calypso, Asx and sba (MDB5/6 homolog) (PubMed:36180891). Interacts (via MBD domain) with Asx (via PHD domain); the interaction is important for the stability of the PR-DUB complex (PubMed:36180891).

(UniProt, A8JR92)

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\sba using the Feature Mapper tool.

External Data

Crossreferences

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

sba_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).

-0.15

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\sba in JBrowse

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

View exonic expression by developmental stage for Dmel\sba

View exonic expression by tissue for Dmel\sba

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

42824/tissue=All

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

FBgn0016754

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0016754

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

FBgn0016754

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

CG13598

Flygut - An atlas of the Drosophila adult midgut

FBgn0016754

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 10 )

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 sba

Transgenic constructs containing regulatory region of sba

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3R)Exel9014

(Ryder, 2004.4.26)

Inferred from location ( 10 )

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

sba^GD8068

viable, with Scer\GAL4^Mef2.PR

sba^GD8068

viable, with Scer\GAL4^pnr-MD237

sba^GD8068

viable, with Scer\GAL4^tin.CΔ4

sba^GD8068

Phenotype manifest in

Allele

wing vein, with Scer\GAL4^Bx-MS1096

sba^EY22988

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) (10)

Hsap\MBD5

6 of 14

Yes

Hsap\MBD6

4 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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\Mbd5

4 of 14

Yes

Rnor\Mbd6

4 of 14

Yes

Rnor\Dnmt3a

1 of 14

Yes

Rnor\Dnmt3b

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (13)

Mmus\Mbd5

5 of 14

Yes

Mmus\Mbd6

4 of 14

Yes

Mmus\Dnmt3a

1 of 14

Yes

Mmus\Dnmt3b

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (7)

Xtro\mbd5

3 of 13

Yes

Xtro\mbd6

3 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (12)

Drer\mbd6

3 of 14

Yes

Drer\dnmt3aa

1 of 14

Yes

Drer\dnmt3ab

1 of 14

Yes

Drer\dnmt3ba

1 of 14

Drer\dnmt3bb.1

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Drer\nsd3

1 of 14

Drer\psip1a

1 of 14

Drer\pwwp2b

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\C06A5.3

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP000707

9 of 12

Yes

Agam\GLYR1_ANOGA

1 of 12

Arabidopsis thaliana (thale-cress) (8)

Atha\AT2G48160

1 of 13

Yes

Atha\AT3G05430

1 of 13

Yes

Atha\AT3G63070

1 of 13

Yes

Atha\AT5G08230

1 of 13

Yes

Atha\AT5G27650

1 of 13

Yes

Atha\ATX1

1 of 13

Yes

Atha\HUA2

1 of 13

Yes

Atha\SDG14

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\SPAC23D3.01

1 of 12

Yes

Spom\SPBC21C3.14c

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:sba. 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)

CG9926

1 of 13

Jasper

1 of 13

Ndf

1 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

MBD5; methyl-CpG binding domain protein 5

model of autosomal dominant intellectual developmental disorder 1

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?

MBD5; methyl-CpG binding domain protein 5

6 of 14

611472

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 1; MRD1

autosomal dominant intellectual developmental disorder 1

MBD6; methyl-CpG binding domain protein 6

4 of 14

619458

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

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

sba - Asx

anti bait coimmunoprecipitation, western blot, molecular sieving, molecular weight estimation by staining, anti tag coimmunoprecipitation, Identification by mass spectrometry

(Tsuboyama et al., 2022)

sba - caly

anti tag coimmunoprecipitation, Identification by mass spectrometry, anti bait coimmunoprecipitation, western blot, molecular sieving, molecular weight estimation by staining

(Tsuboyama et al., 2022)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

G9a

enhanceable

sba

(Kleefstra et al., 2012)

External Data

Subunit Structure (UniProtKB)

(UniProt, A8JR92 )

Linkouts

BioGRID - A database of protein and genetic interactions.

67760

DroID - A comprehensive database of gene and protein interactions.

FBgn0016754

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.

Polycomb repressive complex

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

UCH proteinases

Class of Gene

gene_with_edited_transcript

(Rodriguez et al., 2012)

gene_with_stop_codon_read_through

(Jungreis et al., 2011)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-81

Cytogenetic map

95C9-95C12

Sequence location

3R:23,894,174..23,922,973 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

95C9-95C12

Limits computationally determined from genome sequence between P{PZ}l(3)04684⁰⁴⁶⁸⁴ and P{PZ}Atg6⁰⁰⁰⁹⁶

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

95C6-95C8

(Zeidler, 1996.6.3)

Experimentally Determined Recombination Data

Location

3-81

(FlyBase, 2016)

3-82.4

(Comeron et al., 2012)

(Zeidler, 1996.6.3)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (29)

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

Bloomington

40019

w¹¹¹⁸; P{GMR78H10-GAL4}attP2

40020

w¹¹¹⁸; P{GMR78H12-GAL4}attP2

40342

w¹¹¹⁸; P{GMR82G10-GAL4}attP2

601213

w¹¹¹⁸; P{R78H12-p65.AD}JK22C

54305

w¹¹¹⁸; P{GMR82H04-lexA}attP40

68685

w¹¹¹⁸; P{R78H10-p65.AD}attP40

68686

w¹¹¹⁸; P{R78H10-GAL4.DBD}attP2

Korea

12991

P{VT046525-GAL4}attP2

16331

P{GMR82G10-lexA}JK22C

14256

P{VT046525-lexA::GADfl}attP40

VDRC

v101314

P{KK107527}VIE-260B

v32229

w¹¹¹⁸; P{GD8068}v32229

More stocks available...

Genomic Clones (30)

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

cDNA Clones (26)

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.

FBgn0016754

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0016754

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Tsuboyama et al., 2022)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Mitotic recombination reveals sba has a role in eye development, mutations cause cell death.

(Zeidler and Mlodzik, 1993)

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 (14)

Reported As

Symbol Synonym

AAF56201

(Hendrich and Tweedie, 2003)

CG13598

(Parkhitko et al., 2016, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Misra et al., 2002, Mount, 2001.8.14)

DMTF125

(Kennington et al., 2006)

Dm Sba

(Hendrich and Tweedie, 2003)

F125

(Zeidler and Mlodzik, 1993)

MBD5

(Kleefstra et al., 2012)

SBA

(Tsuboyama et al., 2022)

TF125

(Zeidler, 1996.6.3)

Tf125

dMBD5/6

(Tsuboyama et al., 2022)

sba

(Olivares et al., 2023, Ding et al., 2022, Miozzo et al., 2022, Pun et al., 2022, Bilder et al., 2021, Meltzer et al., 2019, Transgenic RNAi Project members, 2017-, Gene Disruption Project members, 2016-, Gene Disruption Project members, 2015-, Ashwal-Fluss et al., 2014, Iyer et al., 2013, Kleefstra et al., 2012, Rodriguez et al., 2012, Jungreis et al., 2011)

Name Synonyms

TF125 type II

(Zeidler, 1996.8.16)

methyl-CpG-binding domain protein 5/6

(Tsuboyama et al., 2022)

six-banded

(Zeidler and Mlodzik, 1997)

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 ( 55 )

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.

42824

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.

A8JR92

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

A8JR92

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

Q95TH4

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.

A8JR92

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

42824/tissue=All

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

FBgn0016754

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

FBgn0016754

FlyMine - An integrated database for Drosophila genomics

FBgn0016754

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

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

dme:Dmel_CG13598

MARRVEL_MODEL - MARRVEL (model organism gene)

42824

Linkouts

BioGRID - A database of protein and genetic interactions.

67760

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

FBgn0016754

DroID - A comprehensive database of gene and protein interactions.

FBgn0016754

DRSC - Results frm RNAi screens

FBgn0016754

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

sba_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0016754

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0016754

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

CG13598

Flygut - An atlas of the Drosophila adult midgut

FBgn0016754

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

TC000591

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

Polycomb repressive complex

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

UCH proteinases

References (61)

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

-0.15

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