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LOC125371462 Sharpr-MPRA regulatory region 2774 [ Homo sapiens (human) ]

Gene ID: 125371462, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125371462
Gene description
Sharpr-MPRA regulatory region 2774
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, May 2022]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is regulatory element in the vicinity of coronavirus related gene(s).
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Genomic context

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See LOC125371462 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (5861578..5861872)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5849020..5849314)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (5861589..5861883)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene fucosyltransferase 6 Neighboring gene uncharacterized LOC101928844 Neighboring gene fucosyltransferase 3 (Lewis blood group) Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5855126-5855513 Neighboring gene Sharpr-MPRA regulatory region 10376 Neighboring gene fucosyltransferase 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5892267-5893073 Neighboring gene MPRA-validated peak3300 silencer Neighboring gene NADH:ubiquinone oxidoreductase subunit A11 Neighboring gene Sharpr-MPRA regulatory region 9916

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_080732.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    5861578..5861872
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791810.1 Reference GRCh38.p14 PATCHES

    Range
    35159..35453
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    5849020..5849314
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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