FlyBase Gene Report: Dmel\Lim3

General Information

Symbol

Dmel\Lim3

Species

D. melanogaster

Name

Lim3

Annotation Symbol

CG10699

Feature Type

protein_coding_gene

FlyBase ID

FBgn0002023

Gene Model Status

Current

Stock Availability

34 publicly available

Gene Summary

Lim3 (Lim3) encodes a transcription factor that regulates neuronal sub-type identity, including motor neuron identity. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Also Known As

l(2)37Bd

Key Links

Genomic Location

Cytogenetic map

37B13-37C1

Sequence location

2L:19,079,256..19,108,427 [-]

Recombination map

2-54

RefSeq locus

NT_033779 REGION:19079256..19108427

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 (11 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables DNA binding

inferred from electronic annotation with InterPro:IPR001356

(InterPro Project Members, 2004-)

enables DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from electronic annotation with InterPro:IPR017970

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN004680160

(GO Reference Genome Project, 2011-)

enables RNA polymerase II transcription regulatory region sequence-specific DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN004680160

(GO Reference Genome Project, 2011-)

enables zinc ion binding

inferred from electronic annotation with InterPro:IPR049594

(InterPro Project Members, 2004-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in motor neuron axon guidance

inferred from mutant phenotype

(Certel and Thor, 2004)

involved_in positive regulation of gene expression

inferred from mutant phenotype

(Konstantinides et al., 2018)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in nervous system development

traceable author statement

(Skeath and Thor, 2003)

involved_in neuron differentiation

inferred from biological aspect of ancestor with PANTHER:PTN000654232

(GO Reference Genome Project, 2011-)

involved_in regulation of DNA-templated transcription

inferred from electronic annotation with InterPro:IPR017970

(InterPro Project Members, 2004-)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN004680160

(GO Reference Genome Project, 2011-)

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 nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000654232

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

LIM HOMEOBOX TRANSCRIPTION FACTORS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Lim3 (Lim3) encodes a transcription factor that regulates neuronal sub-type identity, including motor neuron identity. [Date last reviewed: 2019-03-14]

Gene Group (FlyBase)

LIM HOMEOBOX TRANSCRIPTION FACTORS -: LIM homeobox transcription factors are sequence-specific DNA binding proteins that regulate transcription. They have two N-terminal LIM domains (cysteine-rich, double-zinc finger motifs) and a centrally located sequence-specific DNA binding homeodomain. (Adapted from PMID:24676471 and FBrf0125444).

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

l(2)37Bd

Larval-pupal lethal; l(2)37Bd2 and l(2)37Bd6 are strong alleles in which second and third instar larvae persist until days eight and nine; few survive to pharate-adult stage with incomplete sclerotization; l(2)37Bd7 similar, but with more pharate adults. l(2)37Bd4 semilethal; l(2)37Bd4/l(2)37Bd7 phenotype similar to that of l(2)37Bd7.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Lim3 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 M9PD53)

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 5.41

Stop-codon suppression (UGA) postulated; FBrf0216884.

Gene model reviewed during 5.44

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

Gene model reviewed during 5.52

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Lim3-RA

FBtr0081170

NM_057258

2562

440

Lim3-RB

FBtr0081169

NM_165277

2677

520

Lim3-RC

FBtr0309832

NM_001259156

3001

520

Lim3-RD

FBtr0309833

NM_001259157

2712

520

Lim3-RE

FBtr0309834

NM_001259158

2284

405

Lim3-RF

FBtr0309835

NM_001259159

3643

520

Lim3-RG

FBtr0329940

NM_001273630

2712

555

Additional Transcript Data and Comments

Reported size (kB)

2.601 (longest cDNA)

(Thor et al., 1999)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Lim3-PA

FBpp0080713

49.0

440

8.06

FBpp0080712

58.4

520

7.93

FBpp0301566

58.4

520

7.93

FBpp0301567

58.4

520

7.93

FBpp0301568

44.9

405

8.21

FBpp0301569

58.4

520

7.93

FBpp0302972

62.4

555

8.05

M9PD53

NP_001260559

AGB93094

Polypeptides with Identical Sequences

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

520 aa isoforms: Lim3-PB, Lim3-PC, Lim3-PD, Lim3-PF

Additional Polypeptide Data and Comments

Reported size (kDa)

440 (aa)

(Thor et al., 1999)

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\Lim3 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).

1.55

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11

neuron of central brain primordium

(De Velasco et al., 2004)

embryonic stage 11 -- 15

stomatogastric nervous system

(De Velasco et al., 2004)

embryonic stage 12

embryonic/larval proventriculus

(Thor et al., 1999)

embryonic/larval alary muscle cell | precursor

(Thor et al., 1999)

dorsal vessel primordium

(Thor et al., 1999)

embryonic stage 12 -- 17

embryonic brain | restricted

(Thor et al., 1999)

larval ventral nerve cord | restricted

(Thor et al., 1999)

presumptive embryonic/larval peripheral nervous system | restricted

(Thor et al., 1999)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic central brain glial cell

(Fisher et al., 2012)

embryonic central brain neuron

(Fisher et al., 2012)

embryonic proventriculus

(Fisher et al., 2012)

gastric caecum

(Fisher et al., 2012)

larval lateral VNC glial cell

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

embryonic stage 14

RP neuron

(Thor et al., 1999)

larval neuron | subset

(Thor et al., 1999)

third instar larval stage

eye disc posterior to the morphogenetic furrow | restricted

(Roignant et al., 2010)

Additional Descriptive Data

Lim3 is expressed in differentiating photoreceptors

(Roignant et al., 2010)

Lim3 expression is observed in several small clusters of neurons in the brain primordium, and in the precursors of the stomatogastric nervous system.

(De Velasco et al., 2004)

In embryos, Lim3 transcript is detected mainly in the nervous system, although expression is also observed in the precursors of the dorsal vessel, alary muscles, and in the proventriculus. Lim3 transcript is first detected in stage 12 embryos, in subsets of cells within the brain, ventral nerve cord, and peripheral nervous system. Expression is not detected in neuroblasts, but in their progeny. In stage 14 embryos, expression is seen in a cluster of 10-12 neurons in each abdominal hemisegment, including RP motor neurons. Studies using reporter constructs indicate that Lim3 expressing cells include a subset of interneurons and motor neurons.

(Thor et al., 1999)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

neuroblast NB1-2

(Lacin and Truman, 2016)

neuroblast NB1-1

(Lacin and Truman, 2016)

neuroblast NB2-2

(Lacin and Truman, 2016)

larval stage

neuron | subset of medulla anlage

(Li et al., 2013)

neuroblast NB1-2

(Lacin and Truman, 2016)

neuroblast NB1-1

(Lacin and Truman, 2016)

neuroblast NB2-2

(Lacin and Truman, 2016)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: Mi{Trojan-GAL4.1}Lim3^{MI03817-TG4.1}

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

distal medullary amacrine neuron Dm10

(Davis et al., 2020)

adult GABAergic neuron | subset

(Davis et al., 2020)

hemilineage 8B secondary neuron

(Allen et al., 2020)

hemilineage 9B secondary neuron

(Allen et al., 2020)

Reporter: P{Lim3.lacZ.T}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 16

larval RP5 motor neuron

(Thor et al., 1999)

larval VO1 motor neuron

(Thor et al., 1999)

motor neuron | subset

(Thor et al., 1999)

larval VO2 motor neuron

(Thor et al., 1999)

larval VL3/4 motor neuron

(Thor et al., 1999)

interneuron | subset

(Thor et al., 1999)

Reporter: P{Lim3.tau-myc.T}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 13

RP neuron

(Thor et al., 1999)

embryonic stage 13 -- 17

motor neuron | subset

(Thor et al., 1999)

embryonic stage 15

motor neuron | subset of larval ventral nerve cord

(Oyallon et al., 2012)

embryonic stage 16

larval RP5 motor neuron

(Thor et al., 1999)

larval VO1 motor neuron

(Thor et al., 1999)

larval VO2 motor neuron

(Thor et al., 1999)

larval VL3/4 motor neuron

(Thor et al., 1999)

interneuron | subset

(Thor et al., 1999)

Reporter: P{Lim3b-GAL4}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 17

embryonic/larval olfactory receptor neuron | subset

Comment: 21h AEL

(Prieto-Godino et al., 2012)

Reporter: P{RK20'-lacZ}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 17

larval RP5 motor neuron

(Wolf et al., 1998)

larval VL3/4 motor neuron

(Wolf et al., 1998)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Lim3 in JBrowse

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

View exonic expression by developmental stage for Dmel\Lim3

View exonic expression by tissue for Dmel\Lim3

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

FBgn0002023

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

35184/tissue=All

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

FBgn0002023

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002023

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

FBgn0002023

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

CG10699

Flygut - An atlas of the Drosophila adult midgut

FBgn0002023

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Lim3

Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 23 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 19 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Lim3

Transgenic constructs containing regulatory region of Lim3

Aberrations (Deficiencies and Duplications) ( 23 )

Inferred from experimentation ( 23 )

Gene disrupted in

Gene duplicated in

Df(2L)TW130

(Certel and Thor, 2004)

Gene not disrupted in

Df(2L)E55

(Stathakis et al., 1995)

Df(2L)hk18

(Wright, 1996, Pentz et al., 1986, Gilbert et al., 1984)

Df(2L)hk-UC1

(Wright, 1996, Stathakis et al., 1995)

Df(2L)OD15

(Wright, 1996, Stathakis et al., 1995, Pentz et al., 1986)

Df(2L)Sd37

(Wright, 1996, Stathakis et al., 1995)

Df(2L)Sd57

(Wright, 1996, Stathakis et al., 1995)

Df(2L)Sd77

(Wright, 1996, Stathakis et al., 1995)

Df(2L)TE37C-1

(Wright, 1996, Gilbert et al., 1984, Wright et al., 1981)

Df(2L)TE37C-7

(Wright, 1996, Stathakis et al., 1995)

Df(2L)TW137

(Stathakis et al., 1995)

Df(2L)TW203

(Wright, 1996, Stathakis et al., 1995, Pentz et al., 1986)

Df(2L)VA12

(Wright, 1996, Stathakis et al., 1995, Pentz et al., 1986, Gilbert et al., 1984, Wright et al., 1981)

Df(2L)VA13

(Wright, 1996, Gilbert et al., 1984, Wright et al., 1981)

Df(2L)VA17

(Wright, 1996, Stathakis et al., 1995, Pentz et al., 1986, Gilbert et al., 1984, Wright et al., 1981)

Df(2L)VA19

(Wright, 1996, Stathakis et al., 1995)

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

lethal | recessive

lethal - all die before end of larval stage | recessive

partially lethal | male limited, with Scer\GAL4^Bx-MS1096

Lim3^{UAS.ORF.GW.Tag:HA}

partially lethal - majority die

Lim3⁴

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

Lim3^GD4742

viable, with Scer\GAL4^Mef2.PR

Lim3^GD4742

viable, with Scer\GAL4^pnr-MD237

Lim3^GD4742

viable, with Scer\GAL4^tin.CΔ4

Lim3^GD4742

Other Phenotypes

Allele

abnormal neuroanatomy (with Df(2L)TW130)

Lim3⁶

abnormal neuroanatomy | dominant

Lim3⁶

short lived

some die during larval stage | recessive

visible, with Scer\GAL4^Bx-MS1096

Lim3^KK108874

visible | female limited, with Scer\GAL4^Bx-MS1096

Lim3^{UAS.ORF.GW.Tag:HA}

Phenotype manifest in

Allele

cuticle & abdomen & pharate adult

cuticle & head & pharate adult

cuticle & thorax & pharate adult

larval abdominal intersegmental nerve

Lim3¹

larval abdominal segmental nerve

Lim3¹

larval intersegmental nerve | embryonic stage 16

Lim3⁶

larval transverse nerve | embryonic stage 16

Lim3⁶

larval transverse nerve | embryonic stage 16 (with Df(2L)TW130)

Lim3⁶

melanotic mass | pharate adult stage

wing, with Scer\GAL4^Bx-MS1096

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) (166)

Hsap\LHX3

12 of 14

Yes

Hsap\LHX4

11 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

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

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

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Hsap\DUX3

1 of 14

Yes

Hsap\DUX5

1 of 14

Yes

Hsap\DUXA

1 of 14

Yes

Hsap\DUXB

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

1 of 14

1 of 14

1 of 14

1 of 14

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

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1 of 14

1 of 14

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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

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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1 of 14

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1 of 14

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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

1 of 14

Yes

1 of 14

1 of 14

1 of 14

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1 of 14

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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) (74)

Rnor\Lhx3

11 of 14

Yes

Rnor\Lhx4

10 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

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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

1 of 14

Mus musculus (laboratory mouse) (88)

Mmus\Lhx3

12 of 14

Yes

Mmus\Lhx4

10 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

1 of 14

1 of 14

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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

1 of 14

1 of 14

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

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

1 of 14

1 of 14

1 of 14

Yes

Mmus\Rhox4a

1 of 14

Yes

Mmus\Rhox4b

1 of 14

Yes

Mmus\Rhox4c

1 of 14

Yes

Mmus\Rhox4d

1 of 14

Yes

Mmus\Rhox4e

1 of 14

Yes

Mmus\Rhox4f

1 of 14

Yes

Mmus\Rhox4g

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

Xenopus tropicalis (Western clawed frog) (123)

Xtro\lhx4

6 of 13

Yes

5 of 13

3 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Xtro\homeobox100496651-provisional

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

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1 of 13

Danio rerio (Zebrafish) (112)

Drer\lhx3

11 of 14

Yes

Drer\lhx4

11 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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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

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

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

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

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

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

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

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

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

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (60)

Cele\ceh-14

9 of 14

Yes

2 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

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

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

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

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

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

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (68)

Agam\AgaP_AGAP009088

12 of 12

Yes

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (34)

Atha\HB-8

2 of 13

Yes

Atha\REV

2 of 13

Yes

Atha\AT4G36860

1 of 13

Atha\ATHB13

1 of 13

Atha\ATHB-15

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\WOX13

1 of 13

Yes

Atha\WOX14

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\PXL1

1 of 13

Yes

Scer\YHP1

1 of 13

Yes

Scer\YOX1

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\phx1

2 of 12

Yes

Spom\rga1

1 of 12

Spom\yox1

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Lim3. 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) (111)

Lim1

5 of 13

4 of 13

Awh

4 of 13

Lmx1a

4 of 13

CG4328

3 of 13

zfh2

3 of 13

bap

2 of 13

bsh

2 of 13

C15

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Dbx

2 of 13

Dll

2 of 13

Drgx

2 of 13

ems

2 of 13

exex

2 of 13

gsb

2 of 13

gsb-n

2 of 13

Gsc

2 of 13

H2.0

2 of 13

hbn

2 of 13

HGTX

2 of 13

HHEX

2 of 13

lbe

2 of 13

lbl

2 of 13

lms

2 of 13

NK7.1

2 of 13

Pax

2 of 13

PHDP

2 of 13

Pph13

2 of 13

prd

2 of 13

Ptx1

2 of 13

repo

2 of 13

tup

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

zen

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

bcd

1 of 13

B-H1

1 of 13

B-H2

1 of 13

btn

1 of 13

cad

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Dfd

1 of 13

esn

1 of 13

eve

1 of 13

exd

1 of 13

eyg

1 of 13

ftz

1 of 13

Hmx

1 of 13

ind

1 of 13

inv

1 of 13

jub

1 of 13

lab

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

otp

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Scr

1 of 13

slou

1 of 13

stck

1 of 13

Tes

1 of 13

toy

1 of 13

Ubx

1 of 13

unc-4

1 of 13

Unc-115a

1 of 13

Unc-115b

1 of 13

vnd

1 of 13

vvl

1 of 13

Zasp52

1 of 13

Zyx

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 ( 2 )

Human Ortholog

Disease

Evidence

References

LHX3; LIM homeobox 3

model of combined pituitary hormone deficiency 3

IEA

(FlyBase, 2019-)

LHX4; LIM homeobox 4

model of combined pituitary hormone deficiency 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?

LHX3; LIM homeobox 3

12 of 14

600577

PITUITARY HORMONE DEFICIENCY, COMBINED, 3; CPHD3

combined pituitary hormone deficiency 3

LHX4; LIM homeobox 4

11 of 14

602146

PITUITARY HORMONE DEFICIENCY, COMBINED, 4; CPHD4

combined pituitary hormone deficiency 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

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

Lim3 - Blos1

two hybrid array

(Shokri et al., 2019)

Lim3 - CG10654

two hybrid array

(Shokri et al., 2019)

Lim3 - CG15286

two hybrid array

(Shokri et al., 2019)

Lim3 - CG18599

two hybrid array

(Shokri et al., 2019)

Lim3 - CG4496

two hybrid array

(Shokri et al., 2019)

Lim3 - Chi

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

Lim3 - GATAd

two hybrid array

(Shokri et al., 2019)

Lim3 - Lpt

two hybrid array

(Shokri et al., 2019)

Lim3 - Rel

two hybrid array

(Shokri et al., 2019)

Lim3 - Ssdp

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

Lim3 - kmg

two hybrid array

(Shokri et al., 2019)

Lim3 - slbo

two hybrid array

(Shokri et al., 2019)

Lim3 - tup

two hybrid array

(Shokri et al., 2019)

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

vvl|Lim3

enhanceable

tup

(Certel and Thor, 2004)

Lim3

enhanceable

vvl

(Certel and Thor, 2004)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

Lim3

(O'Keefe et al., 1998)

tup

enhanceable

Lim3

(Wolfram et al., 2014)

vvl

enhanceable

Lim3

(Certel and Thor, 2004)

vvl|tup

enhanceable

Lim3

(Certel and Thor, 2004)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

61171

DroID - A comprehensive database of gene and protein interactions.

FBgn0002023

MIST (genetic) - An integrated Molecular Interaction Database

35184

MIST (protein-protein) - An integrated Molecular Interaction Database

35184

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

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

2-54

Cytogenetic map

37B13-37C1

Sequence location

2L:19,079,256..19,108,427 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

37B13-37C1

Limits computationally determined from genome sequence between P{lacW}l(2)37Db^k16106&P{lacW}Catsup^k05424 and P{lacW}Ddc^k02104

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

37B-37B

(Thor, 1998.11.24)

Experimentally Determined Recombination Data

Location

2-54

(FlyBase, 2016)

2-53.6

(Comeron et al., 2012)

2-53.9+

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (34)

Genomic Clones (28)

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

FI01025

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.

FBgn0002023

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0002023

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Located between coordinates -37.4 and -13.6.

(Stathakis et al., 1995)

Lim3 mutants affect cuticle formation.

(Black et al., 1987)

larval-pupal lethal

Relationship to Other Genes

Source for database merge of

Source for merge of: Lim3 CG15174

(FlyBase Genome Annotators, 2002-2003)

Additional comments

Annotations CG10699 and CG15174 merged as CG10699 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG10699

(National Institute of Genetics Fly Stocks, 2022-, Ni et al., 2011.7.19, Aerts et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009.3.31, Gandhi et al., 2007, Mount, 2001.8.14)

CG15174

LIM3

(Percival-Smith, 2017)

Lim-3A

(Kanai et al., 2005)

Lim3

(Doe and Thor, 2024, Wang et al., 2024, Kang et al., 2023, Deshpande et al., 2022, National Institute of Genetics Fly Stocks, 2022-, Velten et al., 2022, Davis et al., 2021, Dow et al., 2021, Michki et al., 2021, She et al., 2021, Simon and Konstantinides, 2021, Kitatani et al., 2020, Rybina et al., 2019, Shokri et al., 2019, Bischof et al., 2018, Rybina et al., 2018, Rybina et al., 2017, Transgenic RNAi Project members, 2017-, Bürglin and Affolter, 2016, Gene Disruption Project members, 2016-, Kalay et al., 2016, model organism Encyclopedia of Regulatory Network (modERN) Project, 2015-, Morozova et al., 2015, Naval-Sánchez et al., 2015, Schertel et al., 2015, Kim and Choe, 2014, Lacin et al., 2014, Lacin et al., 2014, Sytnikova et al., 2014, Veselkina et al., 2014, Veselkina et al., 2014, Wolfram et al., 2014, Li et al., 2013, Naval-Sánchez et al., 2013, Turner et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Nose, 2012, Wilczynski et al., 2012, Guest et al., 2011, Jungreis et al., 2011, Stagg et al., 2011, Aerts et al., 2010, Roignant et al., 2010, Rybina and Pasyukova, 2010, Wheeler et al., 2009, Hari et al., 2008, Rybina and Pasyukova, 2008, Roshina and Pasyukova, 2007, Dorner et al., 2006, Jordan et al., 2006, Layden et al., 2006, Wang et al., 2004, McCrady and Tolin, 1994)

Lim3A

(Rybina et al., 2018)

l(2)37Bd

(Stathakis et al., 1995, Black et al., 1987, Wright, 1987)

l(2)Bd

(Wang and Marsh, 1995)

Name Synonyms

Lim3

lethal(2)37Bd

Secondary FlyBase IDs

FBgn0032756

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 68 )

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.

35184

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.

M9PD53

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.

M9PD53

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0002023

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

35184/tissue=All

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

FBgn0002023

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

FBgn0002023

FlyMine - An integrated database for Drosophila genomics

FBgn0002023

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

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

dme:Dmel_CG10699

MARRVEL_MODEL - MARRVEL (model organism gene)

35184

Linkouts

BioGRID - A database of protein and genetic interactions.

61171

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

FBgn0002023

DroID - A comprehensive database of gene and protein interactions.

FBgn0002023

DRSC - Results frm RNAi screens

FBgn0002023

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002023

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0002023

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

CG10699

Flygut - An atlas of the Drosophila adult midgut

FBgn0002023

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

TC014400

MIST (genetic) - An integrated Molecular Interaction Database

35184

MIST (protein-protein) - An integrated Molecular Interaction Database

35184

References (165)

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

1.55

Report Sections