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LOC123464502 Sharpr-MPRA regulatory region 2091 [ Homo sapiens (human) ]

Gene ID: 123464502, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123464502
Gene description
Sharpr-MPRA regulatory region 2091
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (196990798..196991092)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (199717069..199717363)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (196717669..196717963)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene collagen alpha-1(I) chain-like Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196695817-196696352 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196696353-196696888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21106 Neighboring gene 40S ribosomal protein SA-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15082 Neighboring gene ribosomal protein SA pseudogene 30 Neighboring gene MELTF antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196756444-196757080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196757081-196757717 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:196758105-196759304 Neighboring gene melanotransferrin Neighboring gene MPRA-validated peak4992 silencer Neighboring gene discs large MAGUK scaffold protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:196860144-196860342 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:196930580-196931118 Neighboring gene microRNA 4797

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_077487.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    196990798..196991092
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    199717069..199717363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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