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LOC111240478 SLC23A2 promoter P1 [ Homo sapiens (human) ]

Gene ID: 111240478, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111240478
Gene description
SLC23A2 promoter P1
Gene type
biological region
Feature type(s)
mobile_element
protein_bind
regulatory: promoter
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region represents an alternate promoter of the solute carrier family 23 member 2 (SLC23A2) gene, also known as SVCT2. This promoter is activated through synergism among binding of upstream transcription factors (USF1 and 2), nuclear transcription factor Y, and YY1 transcription factor to recognition sites in this sequence. This promoter is derived from sequence related to endogenous retrovirus long terminal repeat (LTR). [provided by RefSeq, Oct 2017]
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Genomic context

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Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (5010028..5010529)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (5049456..5049957)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (4990674..4991175)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372511 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:4760952-4761170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4775280-4776140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4776141-4777001 Neighboring gene Ras association domain family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17498 Neighboring gene uncharacterized LOC107985392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4816447-4816946 Neighboring gene solute carrier family 23 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:4874687-4875187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4877415-4877936 Neighboring gene Sharpr-MPRA regulatory region 14391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12650 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:4953768-4954967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4979144-4979644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12651 Neighboring gene SLC23A2 promoter P2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17504 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:4983486-4984137 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:4984138-4984788 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:5008813-5009342 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:5013735-5013892 Neighboring gene ribosomal protein S21 pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:5025885-5026104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17505 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:5041439-5042638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5046523-5047023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:5053633-5054152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:5054153-5054671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5062418-5062918 Neighboring gene transmembrane protein 230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17509 Neighboring gene RNA, 5S ribosomal pseudogene 474

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Interaction of the transcription start site core region and transcription factor YY1 determine ascorbate transporter SVCT2 exon 1a promoter activity. Qiao H, et al. PLoS One, 2012. PMID 22532872, Free PMC Article
  2. CpG methylation at the USF-binding site mediates cell-specific transcription of human ascorbate transporter SVCT2 exon 1a. Qiao H, et al. Biochem J, 2011 Nov 15. PMID 21770893, Free PMC Article
  3. Functional analysis of two regulatory regions of the human Na+ -dependent vitamin C transporter 2, SLC23A2, in human vascular smooth muscle cells. Rubin SA, et al. Biochim Biophys Acta, 2005 Dec 30. PMID 16380174
  4. Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Cohen CJ, et al. Gene, 2009 Dec 15. PMID 19577618

GeneRIFs: Gene References Into Functions

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 Variation Viewer (GRCh37.p13)

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.

Genomic

  1. NG_055589.1 

    Range
    101..602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    5010028..5010529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    5049456..5049957
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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