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LOC124296658 Sharpr-MPRA regulatory region 9166 [ Homo sapiens (human) ]

Gene ID: 124296658, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124296658
Gene description
Sharpr-MPRA regulatory region 9166
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124296658 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 (73153853..73154147)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (85305289..85305583)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (75768769..75769063)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene cytochrome P450 family 1 subfamily D member 1, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:75681098-75682297 Neighboring gene uncharacterized LOC105376081 Neighboring gene MPRA-validated peak7266 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28464 Neighboring gene CRISPRi-validated cis-regulatory element chr9.871 Neighboring gene CRISPRi-validated cis-regulatory element chr9.872 Neighboring gene annexin A1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:75829932-75830605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28466 Neighboring gene uncharacterized LOC105376082 Neighboring gene uncharacterized LOC101927281

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_078840.1 

    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
    73153853..73154147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    85305289..85305583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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