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LOC113748414 Sharpr-MPRA regulatory region 7220 [ Homo sapiens (human) ]

Gene ID: 113748414, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113748414
Gene description
Sharpr-MPRA regulatory region 7220
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. 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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). It also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [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 (76421132..76421426)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (77709512..77709806)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (76050449..76050743)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:75957380-75957880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:75957881-75958381 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma Neighboring gene ReSE screen-validated silencer GRCh37_chr7:75981845-75982083 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:75987439-75987629 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75987737-75988383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75993799-75994486 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr7:76008919-76009532 and GRCh37_chr7:76009533-76010146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76018334-76019171 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76019172-76020008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:76035061-76035561 Neighboring gene scavenger receptor cysteine rich family member with 4 domains Neighboring gene zona pellucida glycoprotein 3 Neighboring gene Sharpr-MPRA regulatory region 8731 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:76073005-76073916 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:76073917-76074826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76085525-76086398 Neighboring gene deltex E3 ubiquitin ligase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76114631-76115532 Neighboring gene farnesyl diphosphate synthase pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76115533-76116434 Neighboring gene uncharacterized LOC124901675 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:76138251-76138456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76139334-76139906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76139907-76140479 Neighboring gene uroplakin 3B

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

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_062525.1 

    Range
    101..395
    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
    76421132..76421426
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    77709512..77709806
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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