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LOC113748412 Sharpr-MPRA regulatory region 5953 [ Homo sapiens (human) ]

Gene ID: 113748412, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113748412
Gene description
Sharpr-MPRA regulatory region 5953
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 unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (75528039..75528333)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (76815378..76815672)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (75157369..75157663)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NSUN5 pseudogene 1 Neighboring gene 7q11.23 proximal recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18294 Neighboring gene POM121 transmembrane nucleoporin C Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75083199-75083700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18295 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75115301-75115800 Neighboring gene speedy/RINGO cell cycle regulator family member E5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18297 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75160518-75161214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26178 Neighboring gene PMS1 homolog 2, mismatch repair system component pseudogene 3 Neighboring gene huntingtin interacting protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75224249-75225196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75232242-75233192 Neighboring gene MPRA-validated peak6604 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75240777-75241350 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75246639-75247140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75252505-75253458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75253459-75254412 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75260462-75260962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18298 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75268875-75269629 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75269630-75270383 Neighboring gene Sharpr-MPRA regulatory region 13243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26180 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:75359065-75359566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18299 Neighboring gene Sharpr-MPRA regulatory region 12151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26181 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:75407745-75408312 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:75408313-75408880 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:75409977-75410145 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:75416862-75417721 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:75417722-75418580 Neighboring gene C-C motif chemokine ligand 26

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_062523.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    75528039..75528333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    76815378..76815672
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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