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LOC124403975 Sharpr-MPRA regulatory region 3619 [ Homo sapiens (human) ]

Gene ID: 124403975, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124403975
Gene description
Sharpr-MPRA regulatory region 3619
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 DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124403975 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (70265093..70265387)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (71134039..71134333)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72024849..72025143)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S25 pseudogene 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71981496-71981996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71981997-71982497 Neighboring gene inorganic pyrophosphatase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2443 Neighboring gene H3K27me3-DHS negatively-acting regulatory element H2 Neighboring gene neuropeptide FF receptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72042967-72043468 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72051346-72051556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3500 Neighboring gene leucine rich repeat containing 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2444 Neighboring gene Sharpr-MPRA regulatory region 4423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72094756-72095256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3502 Neighboring gene NANOG hESC enhancer GRCh37_chr10:72128656-72129157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72141592-72142211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3504 Neighboring gene centrosomal protein 57 like 1 pseudogene 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_079052.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    70265093..70265387
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    71134039..71134333
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
Molecular Biology Databases