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LOC124625909 Sharpr-MPRA regulatory region 2795 [ Homo sapiens (human) ]

Gene ID: 124625909, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625909
Gene description
Sharpr-MPRA regulatory region 2795
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (12624615..12624909)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (12493774..12494068)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6014 Neighboring gene NANOG hESC enhancer GRCh37_chr12:12737991-12738492 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:12749546-12749780 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:12753351-12754550 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:12761265-12761483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12764179-12764930 Neighboring gene ribosomal protein L21 pseudogene 136 Neighboring gene cAMP responsive element binding protein like 2 Neighboring gene uncharacterized LOC124902880 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:12796246-12797445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6018 Neighboring gene G protein-coupled receptor 19 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:12829332-12830160 Neighboring gene MPRA-validated peak1575 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6025 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4261

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

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_079591.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    12624615..12624909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    12493774..12494068
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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