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LOC123493236 Sharpr-MPRA regulatory region 2565 [ Homo sapiens (human) ]

Gene ID: 123493236, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123493236
Gene description
Sharpr-MPRA regulatory region 2565
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123493236 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (169249518..169249812)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (172609246..172609540)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (170170669..170170963)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377527 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:169991001-169991955 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:169995185-169995684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22131 Neighboring gene SH3 domain containing ring finger 1 Neighboring gene ribosomal protein L6 pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22132 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:170146248-170147447 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:170150634-170151313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:170161764-170162264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:170162265-170162765 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:170172321-170173520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15792 Neighboring gene uncharacterized LOC105377529 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:170211490-170211654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:170232766-170233314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:170256304-170256981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22135 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:170291383-170291609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15794 Neighboring gene NIMA related kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22138

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_077660.1 

    Range
    101..395
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    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    169249518..169249812
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    172609246..172609540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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