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LOC124292577 Sharpr-MPRA regulatory region 15195 [ Homo sapiens (human) ]

Gene ID: 124292577, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124292577
Gene description
Sharpr-MPRA regulatory region 15195
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124292577 in Genome Data Viewer
Location:
9p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (38227052..38227346)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (38250981..38251276)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (38227049..38227343)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene uncharacterized LOC107987064 Neighboring gene MPRA-validated peak7237 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:38213884-38214764 Neighboring gene MPRA-validated peak7238 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:38257983-38258545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:38310912-38311470 Neighboring gene uncharacterized LOC107987065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:38316401-38316900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28413 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:38325532-38326041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28414 Neighboring gene uncharacterized LOC105376040 Neighboring gene Sharpr-MPRA regulatory region 3476 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:38380800-38381748 Neighboring gene Sharpr-MPRA regulatory region 2586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28416 Neighboring gene aldehyde dehydrogenase 1 family member B1

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_078821.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    38227052..38227346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    38250981..38251276
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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