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LOC121811724 Sharpr-MPRA regulatory region 10902 [ Homo sapiens (human) ]

Gene ID: 121811724, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121811724
Gene description
Sharpr-MPRA regulatory region 10902
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121811724 in Genome Data Viewer
Location:
10p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (5493726..5494020)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (5496974..5497268)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (5535689..5535983)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene tubulin alpha like 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2079 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13203 Neighboring gene neuroepithelial cell transforming 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13225 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5509025-5509661 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5511491-5512062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5512063-5512634 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5512635-5513206 Neighboring gene CRISPRi-validated cis-regulatory element chr10.219 Neighboring gene CRISPRi-validated cis-regulatory element chr10.222 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:5535211-5535389 Neighboring gene calmodulin like 5 Neighboring gene CALML3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5567229-5567928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:5567929-5568629 Neighboring gene calmodulin like 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 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_075826.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    5493726..5494020
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    5496974..5497268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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