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LOC123575597 Sharpr-MPRA regulatory region 974 [ Homo sapiens (human) ]

Gene ID: 123575597, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575597
Gene description
Sharpr-MPRA regulatory region 974
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (151225528..151225822)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (151764476..151764770)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (150605089..150605383)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986463 Neighboring gene platelet derived growth factor receptor like 2, pseudogene Neighboring gene coiled-coil domain containing 69 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23446 Neighboring gene uncharacterized LOC105378230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16521 Neighboring gene Sharpr-MPRA regulatory region 9347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16522 Neighboring gene uncharacterized LOC124901115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23455 Neighboring gene ganglioside GM2 activator

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_077857.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    151225528..151225822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    151764476..151764770
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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