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LOC125177527 Sharpr-MPRA regulatory region 5505 [ Homo sapiens (human) ]

Gene ID: 125177527, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177527
Gene description
Sharpr-MPRA regulatory region 5505
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with 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]
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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 (62672308..62672615)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (63542234..63542541)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene tousled like kinase 2 Neighboring gene ribosomal protein S10 pseudogene 26 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:60622822-60623322 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:60636816-60637174 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:60642433-60643632 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:60645420-60645891 Neighboring gene MPRA-validated peak2935 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60696223-60696734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60702756-60703256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60703257-60703757 Neighboring gene uncharacterized LOC107985020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60707912-60708768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60729214-60729925 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60729926-60730636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60731349-60732059 Neighboring gene mannose receptor C-type 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60743431-60744021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60746820-60747579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60747580-60748338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60748658-60749158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60749159-60749659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60757143-60757871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60769301-60769962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60769963-60770624 Neighboring gene RNA, U6 small nuclear 446, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8811 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:60781806-60782032 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:60782895-60783686 Neighboring gene uncharacterized LOC105371855 Neighboring gene membrane associated ring-CH-type finger 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12543

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 12541

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_080582.2 

    Range
    101..408
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    62672308..62672615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    63542234..63542541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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