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

    Gene ID: 96626, updated on 2-Nov-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, Nov 2024]
    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_000002.12Genomic 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 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)

    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_2024_08

    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..110368101
      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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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