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LOC112577476 Sharpr-MPRA regulatory region 155 [ Homo sapiens (human) ]

Gene ID: 112577476, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112577476
Gene description
Sharpr-MPRA regulatory region 155
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC112577476 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (111619527..111620291)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (111634398..111635162)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (112162149..112162913)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene transmembrane and immunoglobulin domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1500 Neighboring gene adenosine A3 receptor Neighboring gene RAP1A, member of RAS oncogene family Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1506 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:112150779-112151472 Neighboring gene long intergenic non-protein coding RNA 1160 Neighboring gene uncharacterized LOC107985184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1186 Neighboring gene MPRA-validated peak362 silencer Neighboring gene RNA, U6 small nuclear 151, pseudogene Neighboring gene keratin 18 pseudogene 57

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 1185

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_060039.2 

    Range
    101..865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    111619527..111620291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    111634398..111635162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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