LIMD1 LIM domain containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LIMD1provided by HGNC
Official Full Name: LIM domain containing 1provided by HGNC
Primary source: HGNC:HGNC:6612
See related: Ensembl:ENSG00000144791 MIM:604543; AllianceGenome:HGNC:6612
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Predicted to enable transcription corepressor activity. Involved in several processes, including negative regulation of hippo signaling; regulation of gene expression; and response to hypoxia. Acts upstream of or within P-body assembly and gene silencing by miRNA. Located in several cellular components, including P-body; adherens junction; and focal adhesion. Part of RISC complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in lung (RPKM 16.2), thyroid (RPKM 9.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (45594751..45686341)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (45610699..45702290)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (45636243..45727833)

Chromosome 3 - NC_000003.12 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

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.
High nuclear expression of HIF1alpha, synergizing with inactivation of LIMD1 and VHL, portray worst prognosis among the bladder cancer patients: association with arsenic prevalence.
Title: High nuclear expression of HIF1α, synergizing with inactivation of LIMD1 and VHL, portray worst prognosis among the bladder cancer patients: association with arsenic prevalence.
findings suggest that LIMD1 is a key regulator of mitotic progression, and that dysregulation of LIMD1 contributes to tumorigenesis
Title: LIMD1 phosphorylation in mitosis is required for mitotic progression and its tumor-suppressing activity.
We show that all three mammalian Ajuba family proteins - AJUBA, LIMD1 and WTIP - exhibit tension-dependent localization to adherens junctions, and that both LATS family proteins, LATS1 and LATS2, exhibit an overlapping tension-dependent junctional localization
Title: Tension-dependent regulation of mammalian Hippo signaling through LIMD1.
Kaposi's sarcoma-associated herpesvirus SOX binds to LIMD1 and shows RNA substrate selectivity
Title: Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX.
The lung tumor suppressor protein LIMD1 is a member of the Zyxin family of adaptor proteins, initially characterized as signal transducers shuttling between the cytoplasm and nucleus. LIMD1 expression promotes tumor growth.
Title: A HIF-LIMD1 negative feedback mechanism mitigates the pro-tumorigenic effects of hypoxia.
Low LIMD1 expression is associated with cervical cancer.
Title: Deregulation of LIMD1-VHL-HIF-1α-VEGF pathway is associated with different stages of cervical cancer.
that the reduced expression of LimD1 and VHL might have synergistic effect on induction of HIF1alpha resulting increased cellular proliferation and progression of the disease.
Title: Over expression of HIF1α is associated with inactivation of both LimD1 and VHL in renal cell carcinoma: Clinical importance.
our data also suggests the importance ofLIMD1 and CDC25A in conjunction with HPV for use as diagnostic and prognostic markers of HNSCC, whereas RBSP3 as a prognostic marker only.
Title: Differential transmission of the molecular signature of RBSP3, LIMD1 and CDC25A in basal/ parabasal versus spinous of normal epithelium during head and neck tumorigenesis: A mechanistic study.
LIMD1 coordinates the assembly of an AGO-TNRC6 containing miRISC complex by binding both proteins simultaneously at distinct interfaces.
Title: Argonaute Utilization for miRNA Silencing Is Determined by Phosphorylation-Dependent Recruitment of LIM-Domain-Containing Proteins.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pol	gag-pol	HIV-1 Pol is identified to have a physical interaction with LIM domains containing 1 (LIMD1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed
retropepsin	gag-pol	HIV-1 PR is identified to have a physical interaction with LIM domains containing 1 (LIMD1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

RH104280 (e-PCR)
- UniSTS:98605

D3S3457 (e-PCR)
- UniSTS:153902

RH46120 (e-PCR)
- UniSTS:48433

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-76912 (e-PCR)
- UniSTS:2393

D15S1477 (e-PCR)
- UniSTS:474482

SHGC-67307 (e-PCR)
- UniSTS:89991

D3S3457 (e-PCR)
- UniSTS:26277

RH120743 (e-PCR)
- UniSTS:132825

SHGC-58616 (e-PCR)
- UniSTS:94429

G15894 (e-PCR)
- UniSTS:69112

RH120782 (e-PCR)
- UniSTS:132862

Gene Ontology Provided by GOA

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	ISS Inferred from Sequence or Structural Similarity more info

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

Component	Evidence Code	Pubs
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
part_of RISC complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in focal adhesion	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay 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

Names: LIM domains containing 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_014240.3 → NP_055055.1 LIM domain-containing protein 1

See identical proteins and their annotated locations for NP_055055.1

Status: VALIDATED

Source sequence(s)

AC098476, AC099539, AJ132408, BC117236, BU428864

Consensus CDS

CCDS2729.1

UniProtKB/Swiss-Prot

Q17RQ1, Q9BQQ9, Q9NQ47, Q9UGP4

UniProtKB/TrEMBL

C9JRJ5

Related

ENSP00000273317.4, ENST00000273317.5

Conserved Domains (4) summary

cd09352
Location:472 → 525

LIM1_Ajuba_like; The first LIM domain of Ajuba-like proteins

cd09355
Location:537 → 589

LIM2_Ajuba_like; The second LIM domain of Ajuba-like proteins

cd09438
Location:597 → 658

LIM3_Ajuba_like; The third LIM domain of Ajuba-like proteins

cl26464
Location:69 → 443

Atrophin-1; Atrophin-1 family