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    SLC12A2-DT SLC12A2 divergent transcript [ Homo sapiens (human) ]

    Gene ID: 644873, updated on 10-Oct-2023

    Summary

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    Official Symbol
    SLC12A2-DTprovided by HGNC
    Official Full Name
    SLC12A2 divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:49565
    See related
    Ensembl:ENSG00000245937 AllianceGenome:HGNC:49565
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LINC01184
    Expression
    Ubiquitous expression in thyroid (RPKM 5.8), prostate (RPKM 4.7) and 25 other tissues See more
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    Genomic context

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    See SLC12A2-DT in Genome Data Viewer
    Location:
    5q23.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (127940440..128083175, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (128460208..128602011, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (127276132..127418867, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 192 Neighboring gene cullin 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23036 Neighboring gene uncharacterized LOC124901059 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:127270427-127271080 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:127344859-127345557 Neighboring gene MPRA-validated peak5458 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23037 Neighboring gene solute carrier family 12 member 2 Neighboring gene POGLUT2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16296 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:127680731-127681930 Neighboring gene fibrillin 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:127772173-127773372 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:127871608-127872538

    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. The Role, Function, and Mechanism of Long Intergenic Noncoding RNA1184 (linc01184) in Colorectal Cancer. Sui YX, et al. Dis Markers, 2021. PMID 33564344, Free PMC Article
    2. GWAS Identifies LINC01184/SLC12A2 as a Risk Locus for Skin and Soft Tissue Infections. Rogne T, et al. J Invest Dermatol, 2021 Aug. PMID 33662382, Free PMC Article
    3. Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. Hodonsky CJ, et al. PLoS Genet, 2017 Apr. PMID 28453575, Free PMC Article
    4. Long non-coding RNAs as surrogate indicators for chemical stress responses in human-induced pluripotent stem cells. Tani H, et al. PLoS One, 2014. PMID 25171338, Free PMC Article
    5. Identification of short-lived long non-coding RNAs as surrogate indicators for chemical stress response. Tani H, et al. Biochem Biophys Res Commun, 2013 Oct 4. PMID 24036268

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GWAS Identifies LINC01184/SLC12A2 as a Risk Locus for Skin and Soft Tissue Infections.
      Title: GWAS Identifies LINC01184/SLC12A2 as a Risk Locus for Skin and Soft Tissue Infections.
    2. The Role, Function, and Mechanism of Long Intergenic Noncoding RNA1184 (linc01184) in Colorectal Cancer.
      Title: The Role, Function, and Mechanism of Long Intergenic Noncoding RNA1184 (linc01184) in Colorectal Cancer.
    3. We also discovered and replicated three genome-wide significant variants in previously unreported loci for RDW (SLC12A2 rs17764730, PSMB5 rs941718), and hematocrit (PROX1 rs3754140) and an upstream anti-sense long-noncoding RNA, LINC01184, as the likely causal variant
      Title: Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos.
    4. six novel lncRNAs (CDKN2B-AS1, MIR22HG, GABPB1-AS1, FLJ33630, LINC00152, and LINC0541471_v2) that respond to model chemical stresses (cycloheximide, hydrogen peroxide, cadmium, or arsenic) in hiPSCs.
      Title: Long non-coding RNAs as surrogate indicators for chemical stress responses in human-induced pluripotent stem cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    EBI GWAS Catalog

    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

    General gene information

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    Markers

    Other Names

    • long intergenic non-protein coding RNA 1184

    Clone Names

    • FLJ33630

    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.

    RNA

    1. NR_015360.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332, BX648677, CD723302
      Related
      ENST00000501702.7

    2. NR_152798.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005352, AC011332, AK090949
      Related
      ENST00000687795.1

    3. NR_152799.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332

    4. NR_152800.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005352, AC011332
      Related
      ENST00000668567.1

    5. NR_152801.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332
      Related
      ENST00000655628.1

    6. NR_152802.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005352, AC011332
      Related
      ENST00000689029.1

    7. NR_152803.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005352, AC011332, DA139927

    8. NR_152804.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005353, AC011332, AC068658, BC036629

    9. NR_152805.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332
      Related
      ENST00000664006.1

    10. NR_152806.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332
      Related
      ENST00000663841.1

    11. NR_152807.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005352, AC011332

    12. NR_152808.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332
      Related
      ENST00000663976.1

    13. NR_152809.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332
      Related
      ENST00000656563.1

    14. NR_152810.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332

    15. NR_152811.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332

    16. NR_152812.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005352, AC011332

    17. NR_152813.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332, AC068658, AF088062

    18. NR_152814.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005352, AC011332, BX385598
      Related
      ENST00000501652.5

    19. NR_152815.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011332
      Related
      ENST00000654888.1

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      127940440..128083175 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      128460208..128602011 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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

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    Research Materials