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LSM12 LSM12 homolog [ Homo sapiens (human) ]

Gene ID: 124801, updated on 10-Dec-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, Dec 2024]
Expression
Ubiquitous expression in testis (RPKM 15.2), placenta (RPKM 11.4) and 25 other tissues See more
Orthologs
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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: 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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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)

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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