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LOC125316800 Sharpr-MPRA regulatory region 14042 [ Homo sapiens (human) ]

Gene ID: 125316800, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316800
Gene description
Sharpr-MPRA regulatory region 14042
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, May 2022]
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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 (76261988..76262282)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (77158544..77158838)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ring finger protein 157 Neighboring gene ATP synthase membrane subunit g pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74235542-74236214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9007 Neighboring gene uncharacterized LOC105371896 Neighboring gene activating transcription factor 4 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74268019-74268543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74268544-74269067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74273189-74274033 Neighboring gene UBA like domain containing 2 Neighboring gene glutamine rich 2 Neighboring gene phosphoribosyl pyrophosphate synthetase associated protein 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

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

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_080619.1 

    Range
    101..395
    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
    76261988..76262282
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    77158544..77158838
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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