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LOC113748391 Sharpr-MPRA regulatory region 11841 [ Homo sapiens (human) ]

Gene ID: 113748391, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113748391
Gene description
Sharpr-MPRA regulatory region 11841
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (4681998..4682375)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (4799197..4799574)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (4721629..4721923)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375133 Neighboring gene MPRA-validated peak6348 silencer Neighboring gene endogenous retrovirus group K member 6 Env polyprotein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4643917-4644418 Neighboring gene Sharpr-MPRA regulatory region 9979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17897 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:4704492-4704666 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:4720927-4721427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4722783-4723310 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4739232-4739732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4742083-4742842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4744443-4745084 Neighboring gene forkhead box K1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4745727-4746368 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4746369-4747010 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4747011-4747652 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4747653-4748294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4748937-4749577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4750899-4751431 Neighboring gene uncharacterized LOC124901581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4763724-4764310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25560

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  2. 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
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 17898

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_062502.2 

    Range
    101..478
    Download
    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
    4681998..4682375
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    4799197..4799574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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