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LOC124292588 Sharpr-MPRA regulatory region 4978 [ Homo sapiens (human) ]

Gene ID: 124292588, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124292588
Gene description
Sharpr-MPRA regulatory region 4978
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124292588 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (69204473..69204767)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (81372272..81372566)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (71819389..71819683)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28445 Neighboring gene Sharpr-MPRA regulatory region 187 Neighboring gene Friedreich ataxia repeat instability region Neighboring gene Sharpr-MPRA regulatory region 4997 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:71660286-71661281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71669749-71670250 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71670251-71670750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71681521-71682120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:71683371-71683870 Neighboring gene frataxin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:71703383-71703883 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71705161-71706130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71731558-71732058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71732059-71732559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71735458-71736416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71745576-71746105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28446 Neighboring gene tight junction protein 2 Neighboring gene uncharacterized LOC124902175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28447 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71856696-71857196 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71857197-71857697 Neighboring gene uncharacterized LOC124902176 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:71897736-71898504 Neighboring gene NANOG hESC enhancer GRCh37_chr9:71898508-71899009 Neighboring gene Sharpr-MPRA regulatory region 15637 Neighboring gene BRAF-activated non-protein coding RNA Neighboring gene endosomal transmembrane epsin interactor 1

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_078832.1 

    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
    69204473..69204767
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    81372272..81372566
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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