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LOC121079955 Sharpr-MPRA regulatory region 5089 [ Homo sapiens (human) ]

Gene ID: 121079955, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121079955
Gene description
Sharpr-MPRA regulatory region 5089
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (108271208..108271502)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (108773749..108774043)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (107606909..107607203)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16217 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:107144233-107144754 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:107144755-107145277 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:107145278-107145799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22874 Neighboring gene RN7SK pseudogene 122 Neighboring gene F-box and leucine rich repeat protein 17 Neighboring gene VISTA enhancer hs1345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22875 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:107413858-107414740 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:107451090-107451859 Neighboring gene Sharpr-MPRA regulatory region 7585 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:107548797-107549630 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:107547963-107548796 Neighboring gene MPRA-validated peak5404 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:107734886-107735518 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:107753479-107753980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:107772642-107773142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:107773143-107773643 Neighboring gene uncharacterized LOC105379114 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:107889945-107890706 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:107890707-107891467 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:107895154-107895781 Neighboring gene NANOG hESC enhancer GRCh37_chr5:107900026-107900717 Neighboring gene ribosomal protein S20 pseudogene 3

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_074173.1 

    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
    108271208..108271502
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    108773749..108774043
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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