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LOC121048712 Sharpr-MPRA regulatory region 8152 [ Homo sapiens (human) ]

Gene ID: 121048712, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121048712
Gene description
Sharpr-MPRA regulatory region 8152
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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See LOC121048712 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (138863387..138863681)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (141604322..141604616)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (138582229..138582523)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta Neighboring gene ribosomal protein L23a pseudogene 40 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14766 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 25 Neighboring gene Sharpr-MPRA regulatory region 9070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138562234-138562975 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138581611-138582152 Neighboring gene CRISPRi-validated cis-regulatory element chr3.4087 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138598027-138598906 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138598907-138599785 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 3 Neighboring gene uncharacterized LOC124906289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14767

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_074082.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    138863387..138863681
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    141604322..141604616
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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