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LOC122965308 Sharpr-MPRA regulatory region 2927 [ Homo sapiens (human) ]

Gene ID: 122965308, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122965308
Gene description
Sharpr-MPRA regulatory region 2927
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122965308 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52450013..52450307)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52482914..52483208)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52484029..52484323)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443693-52444241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19941 Neighboring gene PHD finger protein 7 Neighboring gene VISTA enhancer hs2179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52471583-52472088 Neighboring gene semaphorin 3G Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52478216-52479092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52479093-52479969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52486099-52486919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52490599-52491274 Neighboring gene troponin C1, slow skeletal and cardiac type Neighboring gene nischarin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52505250-52505750

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_077230.1 

    Range
    101..395
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    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    52450013..52450307
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    52482914..52483208
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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