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LOC124403969 Sharpr-MPRA regulatory region 9231 [ Homo sapiens (human) ]

Gene ID: 124403969, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124403969
Gene description
Sharpr-MPRA regulatory region 9231
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 24:Quies, heterochromatin/dead zone). [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 (64360269..64360563)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (65218228..65218522)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (66120029..66120323)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902439 Neighboring gene uncharacterized LOC105378333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:65801475-65801975 Neighboring gene Sharpr-MPRA regulatory region 2403 Neighboring gene Sharpr-MPRA regulatory region 9742 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:65880319-65880911 Neighboring gene DBF4 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:66144462-66145292 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:66145293-66146122 Neighboring gene MPRA-validated peak969 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr10:66266441-66266965 Neighboring gene uncharacterized LOC105378335 Neighboring gene MPRA-validated peak971 silencer Neighboring gene MPRA-validated peak972 silencer Neighboring gene ribosomal protein L17 pseudogene 35 Neighboring gene uncharacterized LOC107984239 Neighboring gene Sharpr-MPRA regulatory region 14987 Neighboring gene cytochrome P450 family 2 subfamily C member 61, pseudogene

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_079046.1 

    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
    64360269..64360563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    65218228..65218522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
Molecular Biology Databases