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LOC124310628 Sharpr-MPRA regulatory region 14358 [ Homo sapiens (human) ]

Gene ID: 124310628, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310628
Gene description
Sharpr-MPRA regulatory region 14358
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (114156409..114156703)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (126355075..126355369)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (116918689..116918983)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116861361-116861896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116875188-116875688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116875689-116876189 Neighboring gene kinesin family member 12 Neighboring gene Sharpr-MPRA regulatory region 2704 Neighboring gene uncharacterized LOC105376225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116915624-116916145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20209 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116925428-116925944 Neighboring gene collagen type XXVII alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116978156-116978656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116980984-116981982 Neighboring gene NANOG hESC enhancer GRCh37_chr9:116986380-116986932 Neighboring gene microRNA 455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116994231-116994732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116994733-116995232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116997162-116997662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116997663-116998163 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106356 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:117038878-117040077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117043569-117044381 Neighboring gene uncharacterized LOC124902252 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:117050487-117051686

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_078910.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    114156409..114156703
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    126355075..126355369
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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