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LOC123477749 Sharpr-MPRA regulatory region 909 [ Homo sapiens (human) ]

Gene ID: 123477749, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477749
Gene description
Sharpr-MPRA regulatory region 909
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 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 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123477749 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (61320331..61320625)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (64758227..64758521)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (62186049..62186343)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2271 Neighboring gene uncharacterized LOC124900173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:62068190-62068762 Neighboring gene ribosomal protein L17 pseudogene 19 Neighboring gene adhesion G protein-coupled receptor L3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:62252700-62253638 Neighboring gene Sharpr-MPRA regulatory region 11493 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:62459979-62460480 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:62512092-62512706 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:62512707-62513321 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:62629970-62630560 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:62630561-62631150 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:62633919-62634780 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:62634781-62635644 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:62635645-62636506 Neighboring gene ribosomal protein S12 pseudogene 9 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:62776506-62777086 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:62777087-62777665 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:62857945-62858479 Neighboring gene ADGRL3 antisense RNA 1 Neighboring gene ribosomal protein S15a pseudogene 17

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_077552.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    61320331..61320625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    64758227..64758521
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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