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LOC121366049 Sharpr-MPRA regulatory region 3516 [ Homo sapiens (human) ]

Gene ID: 121366049, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366049
Gene description
Sharpr-MPRA regulatory region 3516
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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Location:
10p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (31468280..31468574)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (31498027..31498321)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (31757209..31757503)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene zinc finger E-box binding homeobox 1 Neighboring gene POM121 transmembrane nucleoporin like, pseudogene Neighboring gene serine palmitoyltransferase long chain base subunit 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3239 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:31756459-31756960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3240 Neighboring gene MPRA-validated peak919 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31797084-31797592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31797593-31798099 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:31873359-31873859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2277 Neighboring gene uncharacterized LOC105376484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3241 Neighboring gene glutamate dehydrogenase 1 pseudogene 5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31954277-31955148 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31955149-31956018 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31966287-31966838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:31983575-31984136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:31984137-31984698 Neighboring gene macrophage enriched lincRNA repressor of IFN-gamma signaling

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_074399.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    31468280..31468574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    31498027..31498321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
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