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LOC112935925 Sharpr-MPRA regulatory region 8415 [ Homo sapiens (human) ]

Gene ID: 112935925, updated on 15-Mar-2024

Summary

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Gene symbol
LOC112935925
Gene description
Sharpr-MPRA regulatory region 8415
Gene type
biological region
Feature type(s)
regulatory: enhancer
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. The major subregion includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. Another subregion was validated as an 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 16:ElonW, transcriptional elongation, weaker H3K36me3) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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]
Orthologs
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Genomic context

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See LOC112935925 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197711997..197712710)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (200444361..200445074)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (197439209..197439503)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197390351-197390864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197392407-197392920 Neighboring gene rubicon autophagy regulator Neighboring gene microRNA 922 Neighboring gene MPRA-validated peak4996 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21112 Neighboring gene Sharpr-MPRA regulatory region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197463053-197463900 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197466398-197466530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15092 Neighboring gene forty-two-three domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197504526-197504699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197517785-197518499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21120 Neighboring gene leucine rich repeats and calponin homology domain containing 3 Neighboring gene uncharacterized LOC124909482

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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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Homology

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 21113
  • H3K27ac hESC enhancer GRCh37_chr3:197438868-197439488

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_061440.3 

    Range
    101..814
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    197711997..197712710
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    200444361..200445074
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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