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LOC124416874 Sharpr-MPRA regulatory region 13709 [ Homo sapiens (human) ]

Gene ID: 124416874, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416874
Gene description
Sharpr-MPRA regulatory region 13709
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 22:ReprW, weaker Polycomb repression). [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 (95567992..95568286)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (96447186..96447480)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (97327749..97328043)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97000971-97001634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97001635-97002298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3793 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97020155-97020844 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97024067-97024842 Neighboring gene PDZ and LIM domain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2641 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3795 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97054719-97055315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3798 Neighboring gene CRISPRi-validated cis-regulatory element chr10.3436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3799 Neighboring gene Sharpr-MPRA regulatory region 12220 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97106670-97107322 Neighboring gene sorbin and SH3 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3800 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97190228-97190728 Neighboring gene Sharpr-MPRA regulatory region 10569 Neighboring gene VISTA enhancer hs2353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:97291131-97291878 Neighboring gene NANOG hESC enhancer GRCh37_chr10:97299485-97299986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97311480-97312414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97320711-97321473 Neighboring gene Sharpr-MPRA regulatory region 3716 Neighboring gene RPS3A pseudogene 36 Neighboring gene aldehyde dehydrogenase 18 family member A1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2649

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_079096.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    95567992..95568286
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    96447186..96447480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
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