LIMS3 LIM zinc finger domain containing 3 [Homo sapiens (human)]

Gene ID: 96626, updated on 8-Feb-2025

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Summary

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Official Symbol: LIMS3provided by HGNC
Official Full Name: LIM zinc finger domain containing 3provided by HGNC
Primary source: HGNC:HGNC:30047
See related: Ensembl:ENSG00000256977 AllianceGenome:HGNC:30047
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
Also known as: LIMS4; LIMS3L; PINCH-3
Summary: Predicted to enable metal ion binding activity. Predicted to be located in cytoplasm; focal adhesion; and plasma membrane. [provided by Alliance of Genome Resources, Feb 2025]
Expression: Ubiquitous expression in endometrium (RPKM 16.3), adrenal (RPKM 7.0) and 24 other tissues See more
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Genomic context

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See LIMS3 in Genome Data Viewer

Location:: 2q13

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (109898688..109925625)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (110360332..110368101)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (110656265..110683202)

Chromosome 2 - NC_000002.12

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The full length of its cDNA was 963 bp, with a 354-bp open reading frame (ORF), encoding a 117-amino acid protein. PINCH 2 was a splicing isoform of PINCH.
Title: Molecular cloning and characterization of a novel splice variant of the LIM domain family gene, PINCH 2, in human testis.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:485777

RH98188 (e-PCR)
- UniSTS:86675

RH70783 (e-PCR)
- UniSTS:1985

Readthrough LIMS3-LOC440895

Readthrough gene: LIMS3-LOC440895, Included gene: LOC440895

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM and senescent cell antigen-like-containing domain protein 3

Names: LIM and senescent cell antigen-like domains 3; LIM and senescent cell antigen-like-containing domain protein 3-like; LIM and senescent cell antigen-like-containing domain protein 4; LIM-type zinc finger domains 3; particularly interesting new Cys-His protein 3; pinch 2

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_001394901.1 → NP_001381830.1 LIM and senescent cell antigen-like-containing domain protein 3 isoform b

Status: VALIDATED

Source sequence(s)

AC013271

Consensus CDS

CCDS92835.1

UniProtKB/TrEMBL

A0A0J9YXC7

Related

ENSP00000488486.1, ENST00000480744.3

Conserved Domains (5) summary

cd09331
Location:72 → 130

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:133 → 184

LIM2_PINCH; The second LIM domain of protein PINCH

cd09333
Location:197 → 247

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:253 → 306

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:314 → 367

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001426397.1 → NP_001413326.1 LIM and senescent cell antigen-like-containing domain protein 3 isoform c

Status: VALIDATED

Source sequence(s)

CP068276

UniProtKB/TrEMBL

B2R5G4
NM_033514.5 → NP_277049.1 LIM and senescent cell antigen-like-containing domain protein 3 isoform a

See identical proteins and their annotated locations for NP_277049.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the shorter isoform (a).

Source sequence(s)

AF288404, BQ013290, BX108353, CF994716

Consensus CDS

CCDS2084.1

UniProtKB/Swiss-Prot

A0A0A6YYD2, B4DPH6, C9K0W2, P0CW19, P0CW20, Q9HB10

UniProtKB/TrEMBL

B2R5G4

Related

ENSP00000405165.2, ENST00000437679.3

Conserved Domains (1) summary

cl02475
Location:72 → 114

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

RNA

NR_027467.3 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) includes multiple additional 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC013271, AI887629, BC171890, CF994716