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LOC121331341 Sharpr-MPRA regulatory region 15312 [ Homo sapiens (human) ]

Gene ID: 121331341, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121331341
Gene description
Sharpr-MPRA regulatory region 15312
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121331341 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 (107341128..107341422)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (119512882..119513176)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (110103409..110103703)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987110 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:110005805-110007004 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:110011081-110012047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:110020689-110021228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20156 Neighboring gene RAD23 homolog B, nucleotide excision repair protein Neighboring gene uncharacterized LOC124902241 Neighboring gene uncharacterized LOC107987111 Neighboring gene long intergenic non-protein coding RNA 1509 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:110199139-110199809 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:110200480-110201150 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 32

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_074365.1 

    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
    107341128..107341422
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    119512882..119513176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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