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

Gene ID: 96626, updated on 11-Apr-2024

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, Apr 2022]
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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Location:
2q13
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (109898688..109925625)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (110360332..110387257)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (110656265..110683202)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RAN binding protein 2 Neighboring gene uncharacterized LOC100506563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:110546857-110547358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:110549157-110549656 Neighboring gene LIMS3-LOC440895 readthrough Neighboring gene uncharacterized LOC102724848 Neighboring gene 2q13 recombination region Neighboring gene RANBP2 like and GRIP domain containing 5 Neighboring gene uncharacterized LOC105373547 Neighboring gene uncharacterized LOC124907865 Neighboring gene two pore channel 3 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Molecular cloning and characterization of a novel splice variant of the LIM domain family gene, PINCH 2, in human testis. Liu Y, et al. Mol Biotechnol, 2007 Feb. PMID 17435276
  2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Hillier LW, et al. Nature, 2005 Apr 7. PMID 15815621
  3. Molecular Characterization of the Oncogene BTF3 and Its Targets in Colorectal Cancer. Wang H, et al. Front Cell Dev Biol, 2020. PMID 33644029, Free PMC Article
  4. Transcriptome analysis of human gastric cancer. Oh JH, et al. Mamm Genome, 2005 Dec. PMID 16341674
  5. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Suzuki Y, et al. Genome Res, 2004 Sep. PMID 15342556, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough LIMS3-LOC440895

Readthrough gene: LIMS3-LOC440895, Included gene: LOC440895

Homology

Clone Names

  • FLJ38851, FLJ59126, FLJ79109, MGC138438

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)

  1. 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

  2. NM_001426397.1 → NP_001413326.1  LIM and senescent cell antigen-like-containing domain protein 3 isoform c

    Status: VALIDATED

    Source sequence(s)
    CP068276

  3. 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

  1. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    109898688..109925625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    110360332..110387257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0CW19.1 GenPept UniProtKB/Swiss-Prot:P0CW19

Gene LinkOut

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