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LOC121587560 Sharpr-MPRA regulatory region 2952 [ Homo sapiens (human) ]

Gene ID: 121587560, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587560
Gene description
Sharpr-MPRA regulatory region 2952
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 non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121587560 in Genome Data Viewer
Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (72677710..72678004)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (78494187..78494485)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (72711609..72711903)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1572 Neighboring gene uncharacterized LOC124903718 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11096 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11097 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:72660846-72661404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11099 Neighboring gene VISTA enhancer hs20 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:72756067-72756616 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:72756617-72757164 Neighboring gene ZFHX3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:72769685-72770266 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44255 Neighboring gene RNA, U7 small nuclear 90 pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:72804631-72805830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:72822417-72823032 Neighboring gene keratin 18 pseudogene 18 Neighboring gene RNA, U7 small nuclear 71 pseudogene Neighboring gene zinc finger homeobox 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_074847.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    72677710..72678004
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    78494187..78494485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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