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LOC121079950 Sharpr-MPRA regulatory region 6868 [ Homo sapiens (human) ]

Gene ID: 121079950, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121079950
Gene description
Sharpr-MPRA regulatory region 6868
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 unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [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 (90096692..90096986)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (90577145..90577439)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (89392509..89392803)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22774 Neighboring gene NANOG hESC enhancer GRCh37_chr5:89294234-89294791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22775 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:89327783-89328282 Neighboring gene microRNA 3660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:89368757-89369354 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:89369355-89369950 Neighboring gene MPRA-validated peak5346 silencer Neighboring gene long intergenic non-protein coding RNA 1339 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:89504495-89505111 Neighboring gene Sharpr-MPRA regulatory region 5802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22777 Neighboring gene centrin 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_074168.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    90096692..90096986
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    90577145..90577439
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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