Limd1 LIM domains containing 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Limd1provided by MGI
Official Full Name: LIM domains containing 1provided by MGI
Primary source: MGI:MGI:1352502
See related: Ensembl:ENSMUSG00000025239 AllianceGenome:MGI:1352502
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: D9Ertd192e
Summary: Enables transcription corepressor activity. Involved in negative regulation of canonical Wnt signaling pathway; negative regulation of osteoblast differentiation; and osteoblast development. Located in cytoplasm. Is expressed in several structures, including branchial arch; early conceptus; genitourinary system; hemolymphoid system; and telencephalon. Orthologous to human LIMD1 (LIM domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in large intestine adult (RPKM 22.1), spleen adult (RPKM 19.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 F4; 9 74.0 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (123306790..123350617)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (123478661..123521552)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LIMD1 phase separation contributes to cellular mechanics and durotaxis by regulating focal adhesion dynamics in response to force.
Title: LIMD1 phase separation contributes to cellular mechanics and durotaxis by regulating focal adhesion dynamics in response to force.
Limd1 influences not only stress osteoclastogenesis but also osteoblast function and osteoblast progenitor commitment. Together, these data identify Limd1 as a novel regulator of both bone osetoclast and bone osteoblast development and function.
Title: The LIM protein LIMD1 influences osteoblast differentiation and function.
Limd1 regulates AP-1 activation through an interaction with Traf6 to influence osteoclast development
Title: The LIM protein, Limd1, regulates AP-1 activation through an interaction with Traf6 to influence osteoclast development.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126408 (e-PCR)
- UniSTS:163116

AW822033 (e-PCR)
- UniSTS:208469

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within P-body assembly	ISO Inferred from Sequence Orthology more info
involved_in cell migration	ISO Inferred from Sequence Orthology more info
involved_in cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in miRNA-mediated gene silencing by inhibition of translation	ISO Inferred from Sequence Orthology more info
involved_in miRNA-mediated gene silencing by inhibition of translation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within miRNA-mediated post-transcriptional gene silencing	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of hippo signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of hippo signaling	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of hippo signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of osteoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in osteoblast development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to hypoxia	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to hypoxia	ISO Inferred from Sequence Orthology more info
involved_in response to hypoxia	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	ISO Inferred from Sequence Orthology more info
part_of RISC complex	ISO Inferred from Sequence Orthology more info
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	ISO Inferred from Sequence Orthology more info
located_in adherens junction	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in focal adhesion	ISO Inferred from Sequence Orthology more info
located_in focal adhesion	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: LIM domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001410486.1 → NP_001397415.1 LIM domain-containing protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC125254, AC132852
NM_013860.3 → NP_038888.2 LIM domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_038888.2

Status: VALIDATED

Source sequence(s)

AC125254, AC132852

Consensus CDS

CCDS23660.1

UniProtKB/Swiss-Prot

Q8C8G4, Q9CW55, Q9QXD8

Related

ENSMUSP00000026269.3, ENSMUST00000026269.4

Conserved Domains (3) summary

cd09352
Location:464 → 517

LIM1_Ajuba_like; The first LIM domain of Ajuba-like proteins

cd09355
Location:529 → 581

LIM2_Ajuba_like; The second LIM domain of Ajuba-like proteins

cd09438
Location:589 → 650

LIM3_Ajuba_like; The third LIM domain of Ajuba-like proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

123306790..123350617

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036155046.1 → XP_036010939.1 LIM domain-containing protein 1 isoform X2

Conserved Domains (2) summary

PRK04654
Location:92 → 162

PRK04654; sec-independent translocase; Provisional

cl02475
Location:464 → 495

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_011242977.3 → XP_011241279.1 LIM domain-containing protein 1 isoform X3

Conserved Domains (1) summary

PRK04654
Location:92 → 162

PRK04654; sec-independent translocase; Provisional