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LOC125467782 Sharpr-MPRA regulatory region 9263 [ Homo sapiens (human) ]

Gene ID: 125467782, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125467782
Gene description
Sharpr-MPRA regulatory region 9263
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 3:PromF, promoter flanking). [provided by RefSeq, Jun 2022]
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Genomic context

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Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (130103594..130103888)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (128422395..128422689)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373335 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29931 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20983 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20984 Neighboring gene UTP14A small subunit processome component Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:129086824-129087554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:129093062-129093562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20985 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:129117440-129117676 Neighboring gene BCL6 corepressor like 1 Neighboring gene uncharacterized LOC124905216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:129159157-129159656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20988 Neighboring gene Sharpr-MPRA regulatory region 15346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20989 Neighboring gene E74 like ETS transcription factor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20993 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20995 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:129255011-129255220 Neighboring gene RAB33A, member RAS oncogene family Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:129280263-129281462 Neighboring gene apoptosis inducing factor mitochondria associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:129305519-129306473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29941 Neighboring gene zinc finger protein 280C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20998

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_081251.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    130103594..130103888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    128422395..128422689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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