U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SLC9A3-OT1 SLC9A3 3' UTR overlapping transcript 1 [ Homo sapiens (human) ]

    Gene ID: 25845, updated on 10-Oct-2023

    Summary

    Go to the top of the page Help
    Official Symbol
    SLC9A3-OT1provided by HGNC
    Official Full Name
    SLC9A3 3' UTR overlapping transcript 1provided by HGNC
    Primary source
    HGNC:HGNC:24524
    See related
    Ensembl:ENSG00000188242
    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
    PP7080
    Expression
    Broad expression in colon (RPKM 98.5), kidney (RPKM 72.2) and 19 other tissues See more
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    5p15.33
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (470510..472965, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (465319..467774, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (470625..473080, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22293 Neighboring gene EXOC3 antisense RNA 1 Neighboring gene uncharacterized LOC124900930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22294 Neighboring gene exocyst complex component 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85954 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:458642-459841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:472032-472674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:472675-473315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:475243-475883 Neighboring gene SLC9A3 antisense RNA 1 Neighboring gene solute carrier family 9 member A3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85959 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:496057-496580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:515297-515797 Neighboring gene uncharacterized LOC107986395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:526131-526763

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PP7080 expedites the proliferation and migration of lung adenocarcinoma cells via sponging miR-670-3p and regulating UHRF1BP1. Dan W, et al. J Gene Med, 2021 Aug. PMID 33844396
    2. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Antoniali G, et al. Nat Commun, 2017 Oct 6. PMID 28986522, Free PMC Article
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PP7080 expedites the proliferation and migration of lung adenocarcinoma cells via sponging miR-670-3p and regulating UHRF1BP1.
      Title: PP7080 expedites the proliferation and migration of lung adenocarcinoma cells via sponging miR-670-3p and regulating UHRF1BP1.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Other Names

    • CTD-2228K2.5

    Clone Names

    • DKFZp564I1171

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_024158.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AF370427, BC086861
      Related
      ENST00000342584.3

    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
      470510..472965 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      465319..467774 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_015389.1: Suppressed sequence

      Description
      NM_015389.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Miscellaneous