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LOC121009642 Sharpr-MPRA regulatory region 3172 [ Homo sapiens (human) ]

Gene ID: 121009642, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009642
Gene description
Sharpr-MPRA regulatory region 3172
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 DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW). [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 (13461649..13461943)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (13462105..13462399)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (13503149..13503443)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr3:13363927-13364126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13368365-13368866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13368867-13369366 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:13372259-13372426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19486 Neighboring gene nucleoporin 210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13387355-13388236 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13388237-13389120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13389121-13390003 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13390887-13391769 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:13415591-13416092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:13430034-13430534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13432338-13432896 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13440837-13441368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:13441369-13441898 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:13442941-13443441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14085 Neighboring gene NUP210-HDAC11 intergenic CAGE-defined high expression enhancer Neighboring gene PRR3 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:13521871-13522527 Neighboring gene HDAC11 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12997 Neighboring gene histone deacetylase 11

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_074039.1 

    Range
    101..395
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    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
    13461649..13461943
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    13462105..13462399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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