U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 100288798, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Official Symbol
SLC38A4-AS1provided by HGNC
Official Full Name
SLC38A4 antisense RNA 1provided by HGNC
Primary source
HGNC: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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
12q13.11
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (46383676..46652579)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (46343235..46612159)
105.20220307 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

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. 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

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

General gene information

Go to the top of the page Help

Markers

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_125377.1 RNA Sequence

    Status: VALIDATED

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

  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

  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

  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

  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_2023_10

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

Gene LinkOut

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

Molecular Biology Databases