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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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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

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