FlyBase Gene Report: Dmel\lbm

TETRASPANINS -: Tetraspanins (TSP) have four transmembrane domains and two extracellular loops containing specific short motifs, including highly conserved cysteine residues. TSPs are thought to function as scaffolds that bring multiple proteins - including other TSPs, membrane-associated proteins, extracellular and cytosolic proteins - into single membrane region. These regions are called tetraspanin-enriched microdomains. (Adapted from FBrf0227776 and FBrf0152316).

Protein Function (UniProtKB)

Facilitates synapse formation.

(UniProt, Q24188)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\lbm or the JBrowse view of Dmel\lbm 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

Comments on Gene Model

Gene model reviewed during 5.48

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

lbm-RA

FBtr0089033

NM_078915

1029

208

lbm-RB

FBtr0336873

NM_001273828

923

208

Additional Transcript Data and Comments

Reported size (kB)

1.0 (longest cDNA)

(Kopczynski et al., 1996)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

lbm-PA

FBpp0088104

23.0

208

4.62

NP_523639

AAF59302

lbm-PB

FBpp0307822

23.0

208

4.62

NP_001260757

AGB93290

Polypeptides with Identical Sequences

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

208 aa isoforms: lbm-PA, lbm-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

208 (aa)

(Kopczynski et al., 1996)

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\lbm using the Feature Mapper tool.

External Data

Crossreferences

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

lbm_1
lbm_2

Linkouts

Gene Ontology (4 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

synapse assembly

inferred from mutant phenotype

(Kopczynski et al., 1996)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

extracellular region

inferred from direct assay

(Kopczynski et al., 1996)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

extracellular region

inferred from sequence or structural similarity

(Kopczynski et al., 1996)

integral component of membrane

inferred from sequence model

(Fradkin et al., 2002)

inferred from sequence or structural similarity

(Todres et al., 2000)

integral component of plasma membrane

inferred from biological aspect of ancestor with PANTHER:PTN001060286

(assigned by GO_Central )

(Gaudet et al., 2011)

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 12

central brain primordium

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 14

RP neuron

(Kopczynski et al., 1996)

VUM neuron

(Kopczynski et al., 1996)

U neuron

(Kopczynski et al., 1996)

aCC neuron

(Kopczynski et al., 1996)

Additional Descriptive Data

lbm is expressed specifically by motor neurons, such as aCC, RP1-RP5, the three U neurons, and the VUM neurons. It is also expressed transiently and at lower levels in some peripheral sensory neurons.

(Kopczynski et al., 1996)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 16

motor neuron

• axon

(Kopczynski et al., 1996)

Additional Descriptive Data

lbm protein, a cell surface protein, is transiently expressed along the entire length of motor axons, including their growth cones and presynaptic terminals. The protein is present in late embryogenesis,but disappears by third larval instar.

(Kopczynski et al., 1996)

Marker for

Subcellular Localization

CV Term

Evidence

References

extracellular region

inferred from direct assay

(Kopczynski et al., 1996)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\lbm in GBrowse 2

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

View exonic expression by developmental stage for Dmel\lbm

View exonic expression by tissue for Dmel\lbm

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

FBgn0016032

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0016032

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG2374-RA

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

CG2374

Flygut - An atlas of the Drosophila adult midgut

FBgn0016032

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\lbm

Stages(s) 11-12
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 11 )

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 lbm

Transgenic constructs containing regulatory region of lbm

Deletions and Duplications ( 2 )

Disrupted in

Df(2R)Δ42E

(Lin et al., 2005)

Df(2R)Exel6283

(Ryder, 2004.4.26)

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

lbm^GD1843

viable, with Scer\GAL4^Mef2.PR

lbm^GD1843

viable, with Scer\GAL4^pnr-MD237

lbm^GD1843

Other Phenotypes

Allele

neuroanatomy defective

lbm^Y13

neuroanatomy defective, with Scer\GAL4^elav-C155

lbm^EY02692

neuroanatomy defective | embryonic stage

lbm^Y13

Phenotype manifest in

Allele

growth cone

lbm^Y13

presynaptic ribbon

lbm^Y13

RP3 motor neuron

RP3 neuron & synapse

lbm^Y13

synapse

lbm^Y13

synapse, with Scer\GAL4^elav-C155

lbm^EY02692

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (13)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\CD37

1 of 15

Yes

Hsap\CD53

1 of 15

Yes

Hsap\CD63

1 of 15

Yes

Hsap\CD82

1 of 15

Yes

Hsap\TSPAN1

1 of 15

Yes

Hsap\TSPAN4

1 of 15

Yes

Hsap\TSPAN8

1 of 15

Yes

Hsap\TSPAN9

1 of 15

Yes

Hsap\TSPAN16

1 of 15

Yes

Hsap\TSPAN18

1 of 15

Yes

Hsap\TSPAN19

1 of 15

Yes

Hsap\UPK1A

1 of 15

Yes

Hsap\UPK1B

1 of 15

Yes

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (11)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Cd37

1 of 15

Yes

Mmus\Cd53

1 of 15

Yes

Mmus\Cd63

1 of 15

Yes

Mmus\Cd82

1 of 15

Yes

Mmus\Tspan1

1 of 15

Yes

Mmus\Tspan4

1 of 15

Yes

Mmus\Tspan8

1 of 15

Yes

Mmus\Tspan9

1 of 15

Yes

Mmus\Tspan18

1 of 15

Yes

Mmus\Upk1a

1 of 15

Yes

Mmus\Upk1b

1 of 15

Yes

Rattus norvegicus (Norway rat) (10)

Rnor\Cd37

1 of 13

Yes

Rnor\Cd53

1 of 13

Yes

Rnor\Cd63

1 of 13

Yes

Rnor\Cd82

1 of 13

Yes

Rnor\Tspan1

1 of 13

Yes

Rnor\Tspan4

1 of 13

Yes

Rnor\Tspan8

1 of 13

Yes

Rnor\Tspan9

1 of 13

Yes

Rnor\Tspan18

1 of 13

Yes

Rnor\Upk1b

1 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\cd63

1 of 12

Yes

Danio rerio (Zebrafish) (16)

Drer\cd63

1 of 15

Yes

Drer\cd82a

1 of 15

Yes

Drer\cd82b

1 of 15

Yes

Drer\si:ch73-139j3.4

1 of 15

Yes

Drer\tspan4a

1 of 15

Yes

Drer\tspan4b

1 of 15

Yes

Drer\tspan9a

1 of 15

Yes

Drer\tspan9b

1 of 15

Yes

Drer\tspan18a

1 of 15

Yes

Drer\tspan18b

1 of 15

Yes

Drer\tspan34

1 of 15

Yes

Drer\tspan35

1 of 15

Yes

Drer\tspan37

1 of 15

Yes

Drer\upk1a

1 of 15

Yes

Drer\zgc:64051

1 of 15

Yes

Drer\zgc:171713

1 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (9)

Cele\tsp-4

1 of 15

Yes

Cele\tsp-5

1 of 15

Yes

Cele\tsp-6

1 of 15

Yes

Cele\tsp-7

1 of 15

Yes

Cele\tsp-9

1 of 15

Yes

Cele\tsp-11

1 of 15

Yes

Cele\tsp-18

1 of 15

Yes

Cele\tsp-19

1 of 15

Yes

Cele\tsp-21

1 of 15

Yes

Arabidopsis thaliana (thale-cress) (4)

Atha\AT2G20230

1 of 9

Yes

Atha\AT2G20740

1 of 9

Yes

Atha\AT4G28770

1 of 9

Yes

Atha\TOM2A

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190FNS )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA24625

Drosophila persimilis

Dper\GL11147

Drosophila willistoni

Dwil\GK21784

Drosophila virilis

Dvir\GJ15138

Drosophila mojavensis

Dmoj\GI19477

Drosophila grimshawi

Dgri\GH21508

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150BZ3 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17014904

Glossina morsitans

Tsetse fly

Gmor\GMOY003646

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0E3I )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Tribolium castaneum

Red flour beetle

Tcas\TC012488

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0E1V )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Tetranychus urticae

Two-spotted spider mite

Turt\tetur19g01700

Tetranychus urticae

Two-spotted spider mite

Turt\tetur19g01770

Tetranychus urticae

Two-spotted spider mite

Turt\tetur19g01760

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )

No non-Arthropod Metazoa orthologies identified

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (33)

Gene Symbol

Score

Source

Alignment

2 of 10

2 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

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

Comments on Models/Modifiers Based on Experimental Evidence ( 0 )

Disease Associations of Human Orthologs (via DIOPT v7.1 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

Interactions Browser

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

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

kay

suppressible

lbm

(Franciscovich et al., 2008)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0016032

Pathways

Gene Group - Pathway Membership (FlyBase)

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-55

Cytogenetic map

42E6-42E6

Sequence location

2R:7,049,238..7,051,964 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

42E6-42E6

Limits computationally determined from genome sequence between P{lacW}vimar^k16722 and P{lacW}cos^k16101

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

42F1-42F1

(Kopczynski, 1996.2.12)

Experimentally Determined Recombination Data

Location

2-55

(FlyBase, 2016)

2-56.3

(Comeron et al., 2012)

(Kopczynski, 1996.2.12)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (12)

Bloomington

27278

y¹ v¹; P{TRiP.JF02589}attP2

65640

w¹¹¹⁸; PBac{IT.GAL4}lbm^1252-G4

44781

y¹ w^*; Mi{MIC}lbm^MI08469

15583

y¹ w^67c23; P{EPgy2}lbm^EY02692

34173

y¹ w^*; Mi{MIC}lbm^MI01271/SM6a

35459

y¹ sc^* v¹ sev²¹; P{TRiP.GL00385}attP2

d01697

c01253

c02514

v102739

v7936

w¹¹¹⁸; P{GD1843}v7936

v7937

w¹¹¹⁸; P{GD1843}v7937

Genomic Clones (24)

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

cDNA Clones (14)

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequences

BDGP DGC clones

RE57845

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.

FBgn0016032

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0016032

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

35623

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Kopczynski et al., 1996)

Commercially Available Antibodies

Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research

10C9_anti-late_bloomer

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: lbm CG2374

(Shue, 1999.11)

Source for database merge of

Additional comments

Other Comments

Expression is enriched in embryonic gonads.

(Shigenobu et al., 2006)

lbm encodes a neural tetraspanin that facilitates synapse formation.

(Kopczynski et al., 1996)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 34 )

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.

35623

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

Q24188

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

A0A0B4KF78

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0016032

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

FBgn0016032

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

lbm_1
lbm_2

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

CG2374

Flygut - An atlas of the Drosophila adult midgut

FBgn0016032

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

35623

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

TC012488

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

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

Dmel_CG2374

modMine - A data warehouse for the modENCODE project

FBgn0016032

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0016032

DRSC - Results frm RNAi screens

FBgn0016032

Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research

10C9_anti-late_bloomer

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0016032

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG2374-RA

FlyMine - An integrated database for Drosophila genomics

FBgn0016032

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

CG2374

(Ni et al., 2011.7.19, Keleman et al., 2009.8.5, Fradkin et al., 2002, Todres et al., 2000)

Dm.Tsp42Em

(Todres et al., 2000)

Ibm

(Franciscovich et al., 2008)

LBM

(Brooks et al., 2011)

Lbm

(Parchure et al., 2015, Beckett et al., 2013, Koles et al., 2012, Kopczynski et al., 1998)

lbl

(Todres et al., 2000, Lear et al., 1999, Kopczynski, 1996.2.12, Kopczynski et al., 1996)

lbm

(Clandinin and Owens, 2016-, Crocker et al., 2016, Jeibmann et al., 2015, Perkins et al., 2009.8.10, Franciscovich et al., 2008, Shigenobu et al., 2006)

Name Synonyms

Late Bloomer

(Tran and Doe, 2008, Roush, 1996)

Late bloomer

(Parchure et al., 2015, Beckett et al., 2013)

late bloomer

(Jeibmann et al., 2015, Hong et al., 2012, Brooks et al., 2011, Edwards et al., 2009)

latebloomer

(Kamphorst et al., 2002)

tetraspanin 42E

(Silverman et al., 2003)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (57)

Report Sections

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