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LOC123956238 Sharpr-MPRA regulatory region 5293 [ Homo sapiens (human) ]

Gene ID: 123956238, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956238
Gene description
Sharpr-MPRA regulatory region 5293
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 non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (138419484..138419778)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (139729154..139729448)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (138104229..138104523)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ribosomal protein S17 pseudogene 12 Neighboring gene Sharpr-MPRA regulatory region 8802 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4907 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:138062972-138063578 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:138080812-138081666 Neighboring gene prothymosin alpha pseudogene 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:138118122-138118654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:138118655-138119187 Neighboring gene inosine monophosphate dehydrogenase 1 pseudogene 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:138143459-138143969 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:138144373-138145155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18687 Neighboring gene Sharpr-MPRA regulatory region 12555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:138163790-138164350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:138164351-138164911 Neighboring gene small nucleolar RNA U13 Neighboring gene tripartite motif containing 24

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_078432.1 

    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
    138419484..138419778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    139729154..139729448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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