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

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

Summary

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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
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Genomic context

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See SLC9A3-OT1 in Genome Data Viewer
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

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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. 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

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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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Other Names

  • CTD-2228K2.5

Clone Names

  • DKFZp564I1171

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_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

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