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    LSM12 LSM12 homolog [ Homo sapiens (human) ]

    Gene ID: 124801, updated on 28-Oct-2024

    Summary

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    Official Symbol
    LSM12provided by HGNC
    Official Full Name
    LSM12 homologprovided by HGNC
    Primary source
    HGNC:HGNC:26407
    See related
    Ensembl:ENSG00000161654 MIM:611793; AllianceGenome:HGNC:26407
    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
    PNAS-135
    Summary
    Predicted to enable RNA binding activity. Located in cytoplasm. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in testis (RPKM 15.2), placenta (RPKM 11.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LSM12 in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44034328..44067587, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (44886845..44920099, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42111696..42144955, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 11566 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:42091474-42092673 Neighboring gene Sharpr-MPRA regulatory region 15580 Neighboring gene transmembrane protein 101 Neighboring gene uncharacterized LOC124904152 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42102423-42102924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42146518-42147445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42147446-42148372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12251 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42149300-42150225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42152642-42153376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42154394-42154933 Neighboring gene glucose-6-phosphatase catalytic subunit 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:42159496-42160695 Neighboring gene histone deacetylase 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42169749-42170254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42172728-42173488 Neighboring gene Sharpr-MPRA regulatory region 9416 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42176231-42176442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42182651-42183302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42189382-42189882 Neighboring gene uncharacterized LOC105371789

    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. Lsm12 is an NAADP receptor and a two-pore channel regulatory protein required for calcium mobilization from acidic organelles. Zhang J, et al. Nat Commun, 2021 Aug 6. PMID 34362892, Free PMC Article
    2. Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC). Dong Y, et al. J Exp Clin Cancer Res, 2022 Apr 21. PMID 35449073, Free PMC Article
    3. Convergent activation of two-pore channels mediated by the NAADP-binding proteins JPT2 and LSM12. Gunaratne GS, et al. Sci Signal, 2023 Aug 22. PMID 37607218, Free PMC Article
    4. LSM12-EPAC1 defines a neuroprotective pathway that sustains the nucleocytoplasmic RAN gradient. Lee J, et al. PLoS Biol, 2020 Dec. PMID 33362237, Free PMC Article
    5. LSM12 facilitates the progression of colorectal cancer by activating the WNT/CTNNB1 signaling pathway. Zhuang Y, et al. Oncol Res, 2022. PMID 37303493, Free PMC Article

    See all (94) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Convergent activation of two-pore channels mediated by the NAADP-binding proteins JPT2 and LSM12.
      Title: Convergent activation of two-pore channels mediated by the NAADP-binding proteins JPT2 and LSM12.
    2. LSM12 facilitates the progression of colorectal cancer by activating the WNT/CTNNB1 signaling pathway.
      Title: LSM12 facilitates the progression of colorectal cancer by activating the WNT/CTNNB1 signaling pathway.
    3. Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC).
      Title: Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC).
    4. Lsm12 is an NAADP receptor and a two-pore channel regulatory protein required for calcium mobilization from acidic organelles.
      Title: Lsm12 is an NAADP receptor and a two-pore channel regulatory protein required for calcium mobilization from acidic organelles.
    5. LSM12-EPAC1 defines a neuroprotective pathway that sustains the nucleocytoplasmic RAN gradient.
      Title: LSM12-EPAC1 defines a neuroprotective pathway that sustains the nucleocytoplasmic RAN gradient.
    Submit: New GeneRIF Correction

    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

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with LSM12 homolog (LSM12) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Pr55(Gag) gag Interaction of HIV-1 Gag with LSM12 homolog (LSM12) is identified in a series of six affinity purification/mass spectrometry screens 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

    Homology

    Clone Names

    • FLJ30656, MGC104211

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein LSM12
    Names
    protein LSM12 homolog

    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_001369484.1 → NP_001356413.1  protein LSM12 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC023855
      Consensus CDS
      CCDS92334.1
      UniProtKB/TrEMBL
      K7ELG9
      Related
      ENSP00000466074.1, ENST00000585388.2
      Conserved Domains (2) summary
      cd01735
      Location:7 → 67
      LSm12_N; Like-Sm protein 12, N-terminal domain
      smart00995
      Location:78 → 165
      AD; Anticodon-binding domain

    2. NM_001369485.1 → NP_001356414.1  protein LSM12 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC023855
      Conserved Domains (2) summary
      cd01735
      Location:7 → 67
      LSm12_N; Like-Sm protein 12, N-terminal domain
      smart00995
      Location:78 → 197
      AD; Anticodon-binding domain

    3. NM_001369486.1 → NP_001356415.1  protein LSM12 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC023855
      Conserved Domains (2) summary
      smart00995
      Location:28 → 107
      AD; Anticodon-binding domain
      cl00259
      Location:7 → 28
      Sm_like; Sm and related proteins

    4. NM_001371445.1 → NP_001358374.1  protein LSM12 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC023855, AL832076, DR762377, HY010534
      Consensus CDS
      CCDS11475.1
      UniProtKB/Swiss-Prot
      Q3MHD2, Q86YB1, Q96NL5
      Related
      ENSP00000293406.3, ENST00000293406.8
      Conserved Domains (2) summary
      cd01735
      Location:7 → 67
      LSm12_N; Like-Sm protein 12, N-terminal domain
      smart00995
      Location:78 → 165
      AD; Anticodon-binding domain

    5. NM_152344.4 → NP_689557.1  protein LSM12 isoform 3

      See identical proteins and their annotated locations for NP_689557.1

      Status: VALIDATED

      Source sequence(s)
      AC023855
      Consensus CDS
      CCDS11475.1
      UniProtKB/Swiss-Prot
      Q3MHD2, Q86YB1, Q96NL5
      Related
      ENSP00000466718.1, ENST00000591247.6
      Conserved Domains (2) summary
      cd01735
      Location:7 → 67
      LSm12_N; Like-Sm protein 12, N-terminal domain
      smart00995
      Location:78 → 165
      AD; Anticodon-binding domain

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      44034328..44067587 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      44886845..44920099 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3MHD2.2 GenPept UniProtKB/Swiss-Prot:Q3MHD2

    Gene LinkOut

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

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