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LOC114022704 Sharpr-MPRA regulatory region 14989 [ Homo sapiens (human) ]

Gene ID: 114022704, updated on 17-Sep-2024

Summary

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Gene symbol
LOC114022704
Gene description
Sharpr-MPRA regulatory region 14989
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 non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 15:Elon, transcriptional elongation, stronger H3K36me3, more exonic). This repressive element overlaps an intron of the JAK2 (Janus kinase 2) gene, which is relevant for coronavirus biology given its involvement in the cytokine storm inflammatory response. [provided by RefSeq, Jun 2021]
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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See LOC114022704 in Genome Data Viewer
Location:
9p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (5025449..5025743)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (5030533..5030829)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (5025449..5025743)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene RNA terminal phosphate cyclase like 1 Neighboring gene uncharacterized LOC124902113 Neighboring gene microRNA 101-2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28154 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 41 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19749 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:4984323-4985156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28156 Neighboring gene Janus kinase 2 Neighboring gene insulin like 6 Neighboring gene casein kinase 1 gamma 2 pseudogene 1 Neighboring gene decaprenyl diphosphate synthase subunit 1 pseudogene 1

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_063921.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    5025449..5025743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    5030533..5030829
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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