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LOC113875038 Sharpr-MPRA regulatory region 11812 [ Homo sapiens (human) ]

Gene ID: 113875038, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875038
Gene description
Sharpr-MPRA regulatory region 11812
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 1:Tss). [provided by RefSeq, Dec 2018]
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Genomic context

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See LOC113875038 in Genome Data Viewer
Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (71182039..71182333)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (69616131..69616425)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (70401889..70402183)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:70342400-70343599 Neighboring gene mediator complex subunit 12 Neighboring gene uncharacterized LOC124905197 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:70365507-70365762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:70367337-70367883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:70367884-70368430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:70373033-70373532 Neighboring gene neuroligin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29739 Neighboring gene uncharacterized LOC107985688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29741 Neighboring gene gap junction protein beta 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

See Variation Viewer (GRCh37.p13)

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_063226.1 

    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
    71182039..71182333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    69616131..69616425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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