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LOC123477765 Sharpr-MPRA regulatory region 12890 [ Homo sapiens (human) ]

Gene ID: 123477765, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123477765
Gene description
Sharpr-MPRA regulatory region 12890
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 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123477765 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (75555799..75556093)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (78895963..78896257)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (76481009..76481303)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ring finger and CHY zinc finger domain containing 1 Neighboring gene H3K27ac hESC enhancers GRCh37_chr4:76438722-76439652 and GRCh37_chr4:76439653-76440583 Neighboring gene THAP domain containing 6 Neighboring gene uncharacterized LOC124900717 Neighboring gene odontogenesis associated phosphoprotein Neighboring gene cyclin dependent kinase like 2 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 9 Neighboring gene G3BP stress granule assembly factor 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76597475-76598452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21620 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76599431-76600408 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76600409-76601385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21621 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76627962-76628708 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76630201-76630946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:76641306-76641821 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76648951-76649871

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_077568.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    75555799..75556093
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    78895963..78896257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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