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LOC121009652 Sharpr-MPRA regulatory region 2856 [ Homo sapiens (human) ]

Gene ID: 121009652, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009652
Gene description
Sharpr-MPRA regulatory region 2856
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 DNase matched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (16331342..16331636)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (16332537..16332831)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (16372849..16373143)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14113 Neighboring gene oxidoreductase NAD binding domain containing 1 Neighboring gene THAP domain containing 5 pseudogene 2 Neighboring gene uncharacterized LOC107986065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14114 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16343021-16343602 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16343603-16344182 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:16377723-16378222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14115 Neighboring gene raftlin, lipid raft linker 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14116 Neighboring gene uncharacterized LOC124906220 Neighboring gene NANOG hESC enhancer GRCh37_chr3:16497386-16497905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19545 Neighboring gene uncharacterized LOC124906219 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16524187-16525039

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_074043.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    16331342..16331636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    16332537..16332831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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