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LOC112935954 Sharpr-MPRA regulatory region 9847 [ Homo sapiens (human) ]

Gene ID: 112935954, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935954
Gene description
Sharpr-MPRA regulatory region 9847
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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss). [provided by RefSeq, Aug 2018]
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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 (61251255..61251549)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (61294412..61294706)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (61236929..61237223)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene fragile histidine triad diadenosine triphosphatase Neighboring gene uncharacterized LOC124906244 Neighboring gene uncharacterized LOC105377111 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:61015791-61016990 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:61027375-61028574 Neighboring gene Sharpr-MPRA regulatory region 1919 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61126817-61127339 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:61127340-61127863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20020 Neighboring gene Sharpr-MPRA regulatory region 15147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20027 Neighboring gene uncharacterized LOC124909387 Neighboring gene uncharacterized LOC105377114 Neighboring gene uncharacterized LOC105377115 Neighboring gene Sharpr-MPRA regulatory region 1523

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_061468.1 

    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
    61251255..61251549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    61294412..61294706
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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