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LOC112997567 Sharpr-MPRA regulatory region 10925 [ Homo sapiens (human) ]

Gene ID: 112997567, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997567
Gene description
Sharpr-MPRA regulatory region 10925
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112997567 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149611326..149611620)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150146001..150146295)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (148990889..148991183)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene casein kinase 1 alpha 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148924456-148925365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148927595-148928130 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:148929064-148930263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:148931159-148931952 Neighboring gene ribosomal protein L29 pseudogene 14 Neighboring gene Rho guanine nucleotide exchange factor 37 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16498 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23379 Neighboring gene RNA, U6 small nuclear 588, pseudogene Neighboring gene MPRA-validated peak5533 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23382 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:149011522-149012721 Neighboring gene uncharacterized LOC124901104 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23384 Neighboring gene small nucleolar RNA U3

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_061564.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    149611326..149611620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150146001..150146295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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