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LOC124421496 Sharpr-MPRA regulatory region 3016 [ Homo sapiens (human) ]

Gene ID: 124421496, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124421496
Gene description
Sharpr-MPRA regulatory region 3016
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Mar 2022]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is regulatory element in the vicinity of coronavirus related gene(s).
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (13333662..13333956)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (13426419..13426714)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (13355209..13355503)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:13132777-13133277 Neighboring gene uncharacterized LOC124902635 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:13142147-13142764 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:13228795-13229352 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:13282544-13283743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3167 Neighboring gene basic helix-loop-helix ARNT like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4463 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:13362823-13363323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4464 Neighboring gene uncharacterized LOC124902636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:13379341-13379905 Neighboring gene RN7SK pseudogene 151

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_079185.1 

    Range
    101..395
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    13333662..13333956
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    13426419..13426714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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