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

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

    Summary

    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

    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

    Expression

    • 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough LIMS3-LOC440895

    Readthrough gene: LIMS3-LOC440895, Included gene: LOC440895

    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

    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_001394901.1NP_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:72130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314367
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    2. NM_001426397.1NP_001413326.1  LIM and senescent cell antigen-like-containing domain protein 3 isoform c

      Status: VALIDATED

      Source sequence(s)
      CP068276
    3. NM_033514.5NP_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:72114
      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)