Lim3 Lim3 [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: Lim3provided by FlyBase
Official Full Name: Lim3provided by FlyBase
Primary source: FLYBASE:FBgn0002023
Locus tag: Dmel_CG10699
See related: AllianceGenome:FB:FBgn0002023
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: CG10699; CG15174; Dmel\CG10699; l(2)37Bd; l(2)Bd; Lim-3A; lim3; LIM3; Lim3A
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in motor neuron axon guidance and positive regulation of gene expression. Predicted to be active in nucleus. Is expressed in several structures, including CNS glial cell; ganglia; neurons; proventriculus; and segmentally-repeated neuroblast. Human ortholog(s) of this gene implicated in panhypopituitarism. Orthologous to human LHX3 (LIM homeobox 3) and LHX4 (LIM homeobox 4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 37B13-37C1; 2-54 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	2L	NT_033779.5 (19079256..19108427, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	2L	NT_033779.4 (19079256..19108427, complement)

Chromosome 2L - NT_033779.5 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

altered mitochondrial activity is crucial for the decrease of adult lifespan caused by Lim3 knockdown early in life. In adults that encountered Lim3 depletion early in life, the transcription of several genes remained altered, and mitochondrial membrane potential, ATP level and locomotion were increased, confirming the existence of carry-over effects.
Title: Knockdown of the neuronal gene Lim3 at the early stages of development affects mitochondrial function and lifespan in Drosophila.
we demonstrate that the evolutionary conserved Lim3 core promoter provides basic Lim3 expression, whereas structural changes in the Lim3 PRE of distal promoter provide stage-, and tissue-specific Lim3 expression. Therefore, we hypothesize that PcG/TrxG proteins, which are directly involved in Lim3 transcription regulation, participate in lifespan control.
Title: Polycomb/Trithorax group-dependent regulation of the neuronal gene Lim3 involved in Drosophila lifespan control.
These observations provide evidence for combinatorial activity of Isl and Lim3 in regulating ion channel gene expression
Title: The transcription factors islet and Lim3 combinatorially regulate ion channel gene expression.
Polymorphism of Lim3 affects Lim3 transcription and fly lifespan.
Title: A naturally occurring polymorphism at Drosophila melanogaster Lim3 Locus, a homolog of human LHX3/4, affects Lim3 transcription and fly lifespan.
Molecular variation of the shuttle craft and Lim3 genes, controlling the development of the nervous system, in a natural Drosophila melanogaster population
Title: [Molecular variation of the shuttle craft and Lim3 genes, controlling the development of the nervous system, in a natural Drosophila melanogaster population].
the class III POU protein, Drifter (Ventral veinless), is co-expressed with Islet and Lim3 specifically in the ISNb motoneuron subclass
Title: Specification of Drosophila motoneuron identity by the combinatorial action of POU and LIM-HD factors.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in motor neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: Lim3

Names: CG10699-PA; CG10699-PB; CG10699-PC; CG10699-PD; CG10699-PE; CG10699-PF; CG10699-PG; Lim3-PA; Lim3-PB; Lim3-PC; Lim3-PD; Lim3-PE; Lim3-PF; Lim3-PG; lethal(2)37Bd

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NT_033779.5 Reference assembly

Range

19079256..19108427 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001259159.1 → NP_001246088.1 Lim3, isoform F [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001246088.1

Status: REVIEWED

UniProtKB/TrEMBL

Q86P58, Q9VJ00

Conserved Domains (3) summary

cd09368
Location:122 → 173

LIM1_Lhx3_Lhx4; The first LIM domain of Lhx3 and Lhx4 family

cd09376
Location:181 → 236

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

pfam00046
Location:259 → 312

Homeobox; Homeobox domain
NM_165277.3 → NP_724161.1 Lim3, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_724161.1

Status: REVIEWED

UniProtKB/TrEMBL

Q86P58, Q9VJ00

Related

FBpp0080712

Conserved Domains (3) summary

cd09368
Location:122 → 173

LIM1_Lhx3_Lhx4; The first LIM domain of Lhx3 and Lhx4 family

cd09376
Location:181 → 236

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

pfam00046
Location:259 → 312

Homeobox; Homeobox domain
NM_001259156.1 → NP_001246085.1 Lim3, isoform C [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001246085.1

Status: REVIEWED

UniProtKB/TrEMBL

Q86P58, Q9VJ00

Conserved Domains (3) summary

cd09368
Location:122 → 173

LIM1_Lhx3_Lhx4; The first LIM domain of Lhx3 and Lhx4 family

cd09376
Location:181 → 236

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

pfam00046
Location:259 → 312

Homeobox; Homeobox domain
NM_001259157.3 → NP_001246086.1 Lim3, isoform D [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001246086.1

Status: REVIEWED

UniProtKB/TrEMBL

Q86P58, Q9VJ00

Conserved Domains (3) summary

cd09368
Location:122 → 173

LIM1_Lhx3_Lhx4; The first LIM domain of Lhx3 and Lhx4 family

cd09376
Location:181 → 236

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

pfam00046
Location:259 → 312

Homeobox; Homeobox domain
NM_001273630.2 → NP_001260559.1 Lim3, isoform G [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001260559.1

Status: REVIEWED

UniProtKB/TrEMBL

M9PD53, Q86P58

Conserved Domains (3) summary

cd09368
Location:122 → 173

LIM1_Lhx3_Lhx4; The first LIM domain of Lhx3 and Lhx4 family

cd09376
Location:181 → 236

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

pfam00046
Location:259 → 312

Homeobox; Homeobox domain
NM_057258.5 → NP_476606.1 Lim3, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_476606.1

Status: REVIEWED

UniProtKB/TrEMBL

O96686, Q9VJ02

Related

FBpp0080713

Conserved Domains (3) summary

cd09368
Location:42 → 93

LIM1_Lhx3_Lhx4; The first LIM domain of Lhx3 and Lhx4 family

cd09376
Location:101 → 156

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

pfam00046
Location:179 → 232

Homeobox; Homeobox domain
NM_001259158.3 → NP_001246087.1 Lim3, isoform E [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001246087.1

Status: REVIEWED

UniProtKB/TrEMBL

M9NCY1, O96686

Conserved Domains (3) summary

cd09368
Location:7 → 58

LIM1_Lhx3_Lhx4; The first LIM domain of Lhx3 and Lhx4 family

cd09376
Location:66 → 121

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

pfam00046
Location:144 → 197

Homeobox; Homeobox domain