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LOC123956160 Sharpr-MPRA regulatory region 5103 [ Homo sapiens (human) ]

Gene ID: 123956160, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123956160
Gene description
Sharpr-MPRA regulatory region 5103
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 non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956160 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 (73601839..73602133)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (74802720..74803010)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (73016169..73016463)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene BAF chromatin remodeling complex subunit BCL7B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26125 Neighboring gene transducin beta like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73001900-73002400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73002401-73002901 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73017160-73017696 Neighboring gene MLX interacting protein like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73021869-73022452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73049903-73050752 Neighboring gene Sharpr-MPRA regulatory region 8994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73082323-73083318 Neighboring gene VPS37D subunit of ESCRT-I Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26127 Neighboring gene DnaJ heat shock protein family (Hsp40) member C30

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_078354.1 

    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
    73601839..73602133
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    74802720..74803010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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