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LOC112841610 Sharpr-MPRA regulatory region 11 [ Homo sapiens (human) ]

Gene ID: 112841610, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112841610
Gene description
Sharpr-MPRA regulatory region 11
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 DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 4:PromP). 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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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (101779025..101779473)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (104491815..104492263)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (101497869..101498163)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20178 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:101444325-101444936 Neighboring gene PDCL3 pseudogene 4 Neighboring gene centrosomal protein 97 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20180 Neighboring gene neurexophilin and PC-esterase domain family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20184 Neighboring gene Sharpr-MPRA regulatory region 1067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20185 Neighboring gene Sharpr-MPRA regulatory region 7874 Neighboring gene NFKB inhibitor zeta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20186 Neighboring gene MPRA-validated peak4754 silencer Neighboring gene RIG-I dependent antiviral response regulator RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20187

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

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 14577

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_061343.2 

    Range
    101..549
    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
    101779025..101779473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    104491815..104492263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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