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    SLC38A4-AS1 SLC38A4 antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 100288798, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC38A4-AS1provided by HGNC
    Official Full Name
    SLC38A4 antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:56178
    See related
    Ensembl:ENSG00000257261 AllianceGenome:HGNC:56178
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Ubiquitous expression in kidney (RPKM 2.8), thyroid (RPKM 1.7) and 25 other tissues See more
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    Genomic context

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    See SLC38A4-AS1 in Genome Data Viewer
    Location:
    12q13.11
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (46383676..46652579)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (46343235..46612159)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (46777459..47046362)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6245 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46765735-46766438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6248 Neighboring gene SLC38A2 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46776823-46777330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4387 Neighboring gene NANOG hESC enhancer GRCh37_chr12:46780024-46780525 Neighboring gene solute carrier family 38 member 2 Neighboring gene NANOG hESC enhancer GRCh37_chr12:46789058-46789559 Neighboring gene uncharacterized LOC124902923 Neighboring gene NANOG hESC enhancer GRCh37_chr12:46824129-46824630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6249 Neighboring gene Sharpr-MPRA regulatory region 10724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6253 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:46979048-46979802 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:46979803-46980557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46997992-46998511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47011695-47012195 Neighboring gene olfactory receptor family 7 subfamily A member 19 pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:47063431-47064104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:47064118-47064618 Neighboring gene microtubule affinity regulating kinase 3 pseudogene 1 Neighboring gene solute carrier family 38 member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47219240-47219798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47219799-47220356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47225315-47226123

    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. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Xu XR, et al. Proc Natl Acad Sci U S A, 2001 Dec 18. PMID 11752456, Free PMC Article
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
    3. 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. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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)

    General gene information

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    Markers

    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_125377.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AC008014, AC008035, AC025031
      Related
      ENST00000734180.1

    2. NR_125378.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon and contains an alternate internal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC008014, AC025031, AC121337
      Related
      ENST00000734176.1

    3. NR_125379.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon and contains an alternate internal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC008014, AC025031, AC121337
      Related
      ENST00000734175.1

    4. NR_125380.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site at the 5' terminal exon, lacks an exon, and contains an alternate internal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC008014, AC025031, AC121337
      Related
      ENST00000734177.1

    5. NR_125381.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' terminal exon and lacks an exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC008014, AC025031

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      46383676..46652579
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      46343235..46612159
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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