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LOC121530598 Sharpr-MPRA regulatory region 4802 [ Homo sapiens (human) ]

Gene ID: 121530598, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121530598
Gene description
Sharpr-MPRA regulatory region 4802
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121530598 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (81024508..81024802)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (78888154..78888448)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (81316849..81317143)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr15:81289897-81290398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6739 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6741 Neighboring gene umcharacterized LOC128071545 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:81295055-81295939 Neighboring gene microRNA 4514 Neighboring gene talin rod domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9947 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:81353064-81353253 Neighboring gene uncharacterized LOC124903540 Neighboring gene cilia and flagella associated protein 161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9948 Neighboring gene acidic nuclear phosphoprotein 32 family member B pseudogene 3

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_074796.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    81024508..81024802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    78888154..78888448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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