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LOC125446261 Sharpr-MPRA regulatory region 9327 [ Homo sapiens (human) ]

Gene ID: 125446261, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446261
Gene description
Sharpr-MPRA regulatory region 9327
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, Jun 2022]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50083060..50083354)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50589960..50590254)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50437830-50438788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50438789-50439748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50439749-50440706 Neighboring gene interleukin 17 receptor E like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50451079-50451679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13948 Neighboring gene tubulin tyrosine ligase like 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50510246-50511128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50511129-50512010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50512330-50512836 Neighboring gene modulator of VRAC current 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:50523503-50524127 Neighboring gene Mov10 like RNA helicase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19297 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:50578307-50578491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50604117-50604668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13949 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50609993-50610685 Neighboring gene pannexin 2

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_081194.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    50083060..50083354
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    50589960..50590254
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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