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LOC125424403 Sharpr-MPRA regulatory region 14748 [ Homo sapiens (human) ]

Gene ID: 125424403, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125424403
Gene description
Sharpr-MPRA regulatory region 14748
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 22:ReprW, weaker Polycomb repression). [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 (26431143..26431437)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (26893589..26893882)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 495 Neighboring gene NANOG hESC enhancer GRCh37_chr22:26800879-26801395 Neighboring gene RPS3A pseudogene 55 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13568 Neighboring gene aspartate beta-hydroxylase domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:26836513-26836669 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:26837982-26839181 Neighboring gene HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:26866926-26868125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13569 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:26889254-26890453 Neighboring gene SRR1 domain containing Neighboring gene tuftelin interacting protein 11

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

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_081138.1 

    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
    26431143..26431437
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    26893589..26893882
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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