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LOC124375245 Sharpr-MPRA regulatory region 9516 [ Homo sapiens (human) ]

Gene ID: 124375245, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124375245
Gene description
Sharpr-MPRA regulatory region 9516
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 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 (136615317..136615611)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148847405..148847699)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139509769..139510063)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:139444236-139445435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29316 Neighboring gene NOTCH1 associated lncRNA in T cell acute lymphoblastic leukemia 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139458066-139458926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139458927-139459788 Neighboring gene VISTA enhancer hs2207 Neighboring gene uncharacterized LOC124902311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139473242-139473768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139479375-139480026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139493297-139493830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139494899-139495430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139495673-139496524 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:139499139-139499319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139499925-139500774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139501625-139502474 Neighboring gene long intergenic non-protein coding RNA 1451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139524155-139524686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139525219-139525750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139525751-139526282 Neighboring gene uncharacterized LOC105376325 Neighboring gene CRISPRi-validated cis-regulatory element chr9.4291 Neighboring gene uncharacterized LOC102724193 Neighboring gene uncharacterized LOC101928612

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_078966.1 

    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
    136615317..136615611
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148847405..148847699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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