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LOC113939973 Sharpr-MPRA regulatory region 6117 [ Homo sapiens (human) ]

Gene ID: 113939973, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939973
Gene description
Sharpr-MPRA regulatory region 6117
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, May 2022]
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Genomic context

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Location:
19q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (40596903..40597197)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (43417488..43417782)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (41102809..41103103)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene spectrin beta, non-erythrocytic 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:41029231-41029526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10635 Neighboring gene SH3KBP1 binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41108540-41109063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10639 Neighboring gene Sharpr-MPRA regulatory region 12022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41119811-41120358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14659 Neighboring gene latent transforming growth factor beta binding protein 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41128498-41129138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41136805-41137395 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:41142798-41142919 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:41153389-41154370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10641 Neighboring gene Sharpr-MPRA regulatory region 4590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:41194847-41195786 Neighboring gene NUMB like endocytic adaptor protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41196725-41197662 Neighboring gene coenzyme Q8B Neighboring gene RNA, U6 small nuclear 195, pseudogene

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_063754.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    40596903..40597197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    43417488..43417782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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