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LOC112997575 Sharpr-MPRA regulatory region 1765 [ Homo sapiens (human) ]

Gene ID: 112997575, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997575
Gene description
Sharpr-MPRA regulatory region 1765
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. 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 19:H4K20, transcription, primarily H4K20me1, more intronic) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). 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]
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Genomic context

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See LOC112997575 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (171965765..171966087)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (172506096..172506418)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (171392769..171393063)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377725 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:171221789-171222988 Neighboring gene Sharpr-MPRA regulatory region 9260 Neighboring gene uncharacterized LOC107986476 Neighboring gene F-box and WD repeat domain containing 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171349530-171350030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171350031-171350531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171370553-171371052 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:171407408-171407976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171410187-171410959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171433526-171434153 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171435409-171436036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171481332-171482159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171482683-171483182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171482181-171482682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23620 Neighboring gene serine/threonine kinase 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171528850-171529636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171542101-171542601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171571210-171571710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23624 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:171578576-171578751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171591501-171592480 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:171602275-171602501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171606399-171607102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171615213-171615988 Neighboring gene EF-hand calcium binding domain 9

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 active region 23617

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_061573.2 

    Range
    101..423
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    171965765..171966087
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    172506096..172506418
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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