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LOC123956268 Sharpr-MPRA regulatory region 1750 [ Homo sapiens (human) ]

Gene ID: 123956268, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123956268
Gene description
Sharpr-MPRA regulatory region 1750
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956268 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (150336460..150336754)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (151514712..151515006)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150033549..150033843)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene actin related protein 3C Neighboring gene uncharacterized LOC100134040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149745856-149746490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149746491-149747124 Neighboring gene Sharpr-MPRA regulatory region 3139 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149917438-149917972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149917973-149918507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149966003-149966503 Neighboring gene NANOG hESC enhancer GRCh37_chr7:149976749-149977333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149983589-149984090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149984091-149984590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18774 Neighboring gene uncharacterized LOC107986858 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:150044724-150044956 Neighboring gene leucine rich repeat containing 61 Neighboring gene zinc finger BED-type containing 10, pseudogene Neighboring gene retinoic acid receptor responder 2

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_078459.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    150336460..150336754
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    151514712..151515006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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