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LOC124153156 Sharpr-MPRA regulatory region 1046 [ Homo sapiens (human) ]

Gene ID: 124153156, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124153156
Gene description
Sharpr-MPRA regulatory region 1046
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124153156 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (41931071..41931365)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (42205371..42205665)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (41788589..41788883)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ankyrin 1 Neighboring gene uncharacterized LOC105379392 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:41656213-41657412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:41666802-41667754 Neighboring gene Sharpr-MPRA regulatory region 6451 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:41675890-41677089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:41685500-41686057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:41691339-41692069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:41692070-41692799 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:41699113-41699614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:41699615-41700114 Neighboring gene RNA, 7SL, cytoplasmic 149, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr8:41734031-41734243 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:41759247-41759433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27296 Neighboring gene lysine acetyltransferase 6A Neighboring gene small nucleolar RNA SNORD112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19150 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:41909597-41910118 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:41910119-41910639 Neighboring gene Sharpr-MPRA regulatory region 9305 Neighboring gene KAT6A antisense RNA 1 Neighboring gene ribosomal protein L17 pseudogene 30

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_078544.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    41931071..41931365
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    42205371..42205665
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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