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LOC123956149 Sharpr-MPRA regulatory region 9826 [ Homo sapiens (human) ]

Gene ID: 123956149, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956149
Gene description
Sharpr-MPRA regulatory region 9826
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 1:Tss). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (50449871..50450165)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (50611086..50611380)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (50517569..50517863)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene IKAROS family zinc finger 1 Neighboring gene uncharacterized LOC124901631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50477534-50478034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26007 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:50488572-50489105 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:50514049-50515248 Neighboring gene RNA, U6 small nuclear 1091, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18183 Neighboring gene fidgetin like 1 Neighboring gene VISTA enhancer hs2059 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr7:50569579-50570080 and GRCh37_chr7:50570081-50570580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50581285-50581919 Neighboring gene dopa decarboxylase Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_99424 and experimental_99425 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:50598907-50600106 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:50602470-50603669 Neighboring gene DDC antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:50637965-50638490 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99443 Neighboring gene growth factor receptor bound protein 10 Neighboring gene uncharacterized LOC124901632

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_078344.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    50449871..50450165
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    50611086..50611380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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