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LOC112272549 Sharpr-MPRA regulatory region 4541 [ Homo sapiens (human) ]

Gene ID: 112272549, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272549
Gene description
Sharpr-MPRA regulatory region 4541
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 matched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (67680992..67681286)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (61888114..61888408)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (68147709..68148003)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene gephyrin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5866 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:68161998-68162634 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8585 Neighboring gene RNA, 5S ribosomal pseudogene 386 Neighboring gene cytochrome c oxidase subunit 7A2 pseudogene 1 Neighboring gene RNA, 7SL, cytoplasmic 369, pseudogene Neighboring gene vesicle transport through interaction with t-SNAREs 1B Neighboring gene ribosomal protein L21 pseudogene 9 Neighboring gene retinol dehydrogenase 11 Neighboring gene retinol dehydrogenase 12

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_056687.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    67680992..67681286
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    61888114..61888408
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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