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LOC121725212 Sharpr-MPRA regulatory region 6875 [ Homo sapiens (human) ]

Gene ID: 121725212, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725212
Gene description
Sharpr-MPRA regulatory region 6875
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 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (107598968..107599262)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (108101822..108102116)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (106934669..106934963)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:106620899-106622098 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:106737319-106737856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22862 Neighboring gene ephrin A5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:106801251-106801752 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:106808214-106808968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22863 Neighboring gene NANOG hESC enhancer GRCh37_chr5:106834891-106835392 Neighboring gene Sharpr-MPRA regulatory region 8638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16212 Neighboring gene NANOG hESC enhancer GRCh37_chr5:106855351-106855852 Neighboring gene uncharacterized LOC124901038 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:106903957-106904492 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:106906417-106907128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22867 Neighboring gene Sharpr-MPRA regulatory region 13332 Neighboring gene VISTA enhancer hs1734 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:106924851-106925777 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:106946073-106947272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:107008991-107009490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16216 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:107031758-107032266 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:107060476-107061675 Neighboring gene ubiquitin specific peptidase 7 (herpes virus-associated) pseudogene Neighboring gene RNA, 7SL, cytoplasmic 782, pseudogene

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_075686.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    107598968..107599262
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    108101822..108102116
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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