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LOC121587571 Sharpr-MPRA regulatory region 13848 [ Homo sapiens (human) ]

Gene ID: 121587571, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587571
Gene description
Sharpr-MPRA regulatory region 13848
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. The major subregion includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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:
17p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (4365316..4366845)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4254579..4256108)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4269809..4270103)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 G1 Neighboring gene major facilitator superfamily domain containing 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4220485-4221252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4236451-4237364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4240300-4241080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11538 Neighboring gene RNA, 7SL, cytoplasmic 774, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11539 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4286079-4286578 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8037 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4298989-4299759 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4299760-4300529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4315987-4316488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4337297-4337951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4342684-4343184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4351479-4351979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4353153-4353653 Neighboring gene SPNS lysolipid transporter 3, sphingosine-1-phosphate (putative) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4379777-4380645 Neighboring gene uncharacterized LOC124903899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4384268-4385023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11541 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4392946-4394145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8039 Neighboring gene SPNS2 antisense RNA 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. 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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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 8035
  • ATAC-STARR-seq lymphoblastoid silent region 8036
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4269303-4269989

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_074859.3 

    Range
    101..1630
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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
    4365316..4366845
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4254579..4256108
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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