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LOC124416861 Sharpr-MPRA regulatory region 10398 [ Homo sapiens (human) ]

Gene ID: 124416861, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416861
Gene description
Sharpr-MPRA regulatory region 10398
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 16:ElonW, transcriptional elongation, weaker H3K36me3). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (86438012..86438306)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87318547..87318842)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88197769..88198063)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene glutamate ionotropic receptor delta type subunit 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88024064-88024564 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17795 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88051161-88051975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88051976-88052790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88057946-88058446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88089455-88090419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88091551-88092052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88092053-88092552 Neighboring gene microRNA 346 Neighboring gene Sharpr-MPRA regulatory region 9256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88122633-88123146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88123147-88123660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2558 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88136831-88137373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2563 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88159531-88160524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88160525-88161518 Neighboring gene uncharacterized LOC124902473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88162319-88162871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3689 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88183258-88184012 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17841 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88221644-88222250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88263469-88263969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2570 Neighboring gene RNA, U6 small nuclear 780, pseudogene Neighboring gene WAPL cohesin release factor Neighboring gene WAPL divergent transcript

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_079083.1 

    Range
    101..395
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    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    86438012..86438306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    87318547..87318842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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