FlyBase Gene Report: Dmel\lmgB

General Information

Symbol

Dmel\lmgB

Species

D. melanogaster

Name

lemming B

Annotation Symbol

CG34441

Feature Type

protein_coding_gene

FlyBase ID

FBgn0085470

Gene Model Status

Current

Stock Availability

10 publicly available

Gene Summary

lemming B (lmgB) encodes is part of the dicistronic lemming locus with two open reading frames (ORFs): lmgA (upstream ORF) and lmgB (downstream ORF). The lmgB ORF codes for a putative polypeptide of 365 amino acids that appears to be conserved in Drosophilidae but not in other species. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Also Known As

APC11

Key Links

Genomic Location

Cytogenetic map

29D4-29D5

Sequence location

2L:8,524,999..8,528,618 [-]

Recombination map

2-33

RefSeq locus

NT_033779 REGION:8524999..8528618

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 (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

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 (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Leucine rich adaptor protein 1/25

Summaries

Gene Snapshot

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\lmgB 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 Q9VLJ5)

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 5.48

Gene model reviewed during 5.46

Gene model reviewed during 5.54

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

lmgB-RA

FBtr0112744

NM_001103654

2953

365

lmgB-RB

FBtr0112745

NM_001103655

2014

365

lmgB-RC

FBtr0333420

NM_001273330

3507

365

lmgB-RD

FBtr0336886

NM_001273331

1462

365

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

lmgB-PA

FBpp0111656

37.7

365

10.37

FBpp0111657

37.7

365

10.37

FBpp0305612

37.7

365

10.37

FBpp0307834

37.7

365

10.37

Q9VLJ5

NP_001260260

AGB92796

Polypeptides with Identical Sequences

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

365 aa isoforms: lmgB-PA, lmgB-PB, lmgB-PC, lmgB-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Leucine rich adaptor protein 1/25

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VLJ5

Mapped Features

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

External Data

Crossreferences

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

lmgB_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).

-0.26

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage -- embryonic stage

organism

(Nagy et al., 2012)

Additional Descriptive Data

lmgB transcripts are seen at all stages of development tested with the highest levels in late pupae and persisting into adults. Levels of mono- and dicistronic lmg transcripts are very similar.

(Nagy et al., 2012)

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\lmgB in JBrowse

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

View exonic expression by developmental stage for Dmel\lmgB

View exonic expression by tissue for Dmel\lmgB

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

FBgn0250903

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

44128/tissue=All

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

FBgn0085470

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

FBgn0085470

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

CG18042

Flygut - An atlas of the Drosophila adult midgut

FBgn0085470

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 6 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of lmgB

Transgenic constructs containing regulatory region of lmgB

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene partially disrupted in

Df(2L)lmg¹³⁸

(Nagy et al., 2012)

Gene disrupted in

Df(2L)lmg^J023

(Nagy et al., 2012)

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.

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) (6)

Hsap\FAM89B

6 of 14

Yes

3 of 14

1 of 14

1 of 14

1 of 14

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) (5)

Rnor\Fam89b

6 of 14

Yes

Rnor\Fam89a

3 of 14

Yes

Rnor\Anapc11

1 of 14

Rnor\Rnf7

1 of 14

Rnor\Trank1

1 of 14

Yes

Mus musculus (laboratory mouse) (6)

Mmus\Fam89b

6 of 14

Yes

Mmus\Fam89a

3 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\fam89a

2 of 13

Yes

Danio rerio (Zebrafish) (4)

Drer\fam89b

6 of 14

Yes

Drer\fam89a

3 of 14

Yes

Drer\rbx1

1 of 14

Drer\rnf7

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (3)

Cele\apc-11

1 of 14

Yes

Cele\rbx-1

1 of 14

Yes

Cele\rbx-2

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP005562

1 of 12

Yes

Agam\AgaP_AGAP008196

1 of 12

Yes

Agam\AgaP_AGAP008197

1 of 12

Yes

Arabidopsis thaliana (thale-cress) (4)

Atha\APC11

1 of 13

Yes

Atha\AT3G42830

1 of 13

Yes

Atha\AT5G26640

1 of 13

Yes

Atha\RBX1

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\APC11

1 of 13

Yes

Scer\HRT1

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\apc11

1 of 12

Yes

Spom\rbx1

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:lmgB. 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) (5)

4 of 13

1 of 13

1 of 13

1 of 13

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 ( 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?

FAM89B; family with sequence similarity 89 member B

6 of 14

616128

FAM89A; family with sequence similarity 89 member A

3 of 14

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

Summary of Genetic Interactions

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.

68849

DroID - A comprehensive database of gene and protein interactions.

FBgn0085470

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_dicistronic_mRNA

(FlyBase Genome Annotators, 2007)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-33

Cytogenetic map

29D4-29D5

Sequence location

2L:8,524,999..8,528,618 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

29D4-29D5

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-33

(FlyBase, 2016)

2-28.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (10)

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

Bloomington

40857

y¹ v¹; P{TRiP.HMS02024}attP40/CyO

11330

P{PZ}lmgA⁰³⁴²⁴ lmgB⁰³⁴²⁴ cn¹/CyO; ry⁵⁰⁶

21361

y¹ w^67c23; P{EPgy2}lmgA^EY11317 lmgB^EY11317/CyO

35936

y¹ w^*; Mi{MIC}Acer^MI01059 lmgA^MI01059 lmgB^MI01059

FlyORF

F001269

M{UAS-lmgB.ORF}ZH-86Fb

F001100

M{UAS-lmgB.ORF.3xHA}ZH-86Fb

NIG-Fly

M2L-1742

y¹ w¹¹¹⁸; lmgB^SK2 P{neoFRT}40A/CyO-Tb

M2L-1743

y¹ w¹¹¹⁸; lmgB^SK5 P{neoFRT}40A/CyO-Tb

2LG-1383

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

VDRC

v103649

P{KK107738}VIE-260B

Genomic Clones (19)

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

cDNA Clones (418)

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

AT07979

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.

FBgn0085470

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0085470

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Additional comments

The "lemming" locus gives rise to a dicistronic transcript. The two open reading frames (ORFs) are lmgA (upstream ORF) and lmgB (downstream ORF). The lethal, morphological and mitotic phenotypes of the Df(2L)lmg¹³⁸ deletion (which affects both open reading frames) are rescued by expression of the lmgA ORF alone and the lmgB ORF does not appear to be efficiently translated in S2 cells.

(Nagy et al., 2012)

Source for split of: CG18042

(FlyBase Genome Annotators, 2007)

Annotation CG18042 split into CG34440 and CG34441 in release 5.2 of the genome

(FlyBase Genome Annotators, 2007)

annotation.

(FlyBase Genome Annotators, 2007)

One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by lmg (CG34440) and CG34441 (CG34441).

(FlyBase Genome Annotators, 2007)

Nomenclature History

Source for database identify of

Source for identity of: lmgB CG34441

(Nagy et al., 2012)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

APC11

(Martins et al., 2017, Weber and Mlodzik, 2017)

CG34441

(National Institute of Genetics Fly Stocks, 2022-, Nagy et al., 2012, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, FlyBase Genome Annotators, 2007)

Dromel_CG18042_FBtr0079695_lmg_mORF

(Hayden and Bosco, 2008)

ORF2

(Nagy et al., 2012)

lmgB

(Weber and Mlodzik, 2017, Bischof, 2014.10.20, Nagy et al., 2012)

Name Synonyms

LemmingB

(Martins et al., 2017)

lemming B

Secondary FlyBase IDs

FBan0018042
FBgn0029004

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 36 )

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.

44128

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.

Q9VLJ5

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

Q9VLJ5

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.

Q9VLJ5

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0250903

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

44128/tissue=All

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

FBgn0085470

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

FBgn0085470

FlyMine - An integrated database for Drosophila genomics

FBgn0085470

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

Leucine rich adaptor protein 1/25

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

dme:Dmel_CG34441

MARRVEL_MODEL - MARRVEL (model organism gene)

44128

Linkouts

BioGRID - A database of protein and genetic interactions.

68849

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

FBgn0085470

DroID - A comprehensive database of gene and protein interactions.

FBgn0085470

DRSC - Results frm RNAi screens

FBgn0085470

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

lmgB_1

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0085470

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

CG18042

Flygut - An atlas of the Drosophila adult midgut

FBgn0085470

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

TC007458

References (20)

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

-0.26

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