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LOC121587586 Sharpr-MPRA regulatory region 11348 [ Homo sapiens (human) ]

Gene ID: 121587586, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587586
Gene description
Sharpr-MPRA regulatory region 11348
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K4me1 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 DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (31525391..31526240)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (32471168..32472017)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (29852409..29852703)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RAB11 family interacting protein 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29794364-29795058 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:29796711-29797212 Neighboring gene RNA, 7SL, cytoplasmic 79, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29803345-29804161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29825931-29826892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29826893-29827852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12013 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29836658-29837448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29850121-29850755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29851414-29852028 Neighboring gene RNA, 7SL, cytoplasmic 45, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12016 Neighboring gene microRNA 4724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8412 Neighboring gene tRNA-Thr (anticodon CGT) 4-1

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. 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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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr17:29852644-29853258

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_074874.2 

    Range
    101..950
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    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    31525391..31526240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    32471168..32472017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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