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LOC121331325 Sharpr-MPRA regulatory region 8240 [ Homo sapiens (human) ]

Gene ID: 121331325, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121331325
Gene description
Sharpr-MPRA regulatory region 8240
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 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 5:Enh, candidate strong enhancer, open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121331325 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 (34644912..34645206)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (34663431..34663725)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (34644909..34645203)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:34624191-34624739 Neighboring gene AT-rich interaction domain 3C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19851 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19853 Neighboring gene sigma non-opioid intracellular receptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28314 Neighboring gene galactose-1-phosphate uridylyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:34654819-34655434 Neighboring gene interleukin 11 receptor subunit alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:34659625-34660126 Neighboring gene C-C motif chemokine ligand 27

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_074349.1 

    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
    34644912..34645206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    34663431..34663725
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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