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LOC121587539 Sharpr-MPRA regulatory regions 5680 and 15498 [ Homo sapiens (human) ]

Gene ID: 121587539, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587539
Gene description
Sharpr-MPRA regulatory regions 5680 and 15498
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. Two overlapping subregions were validated as functional enhancers 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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (27538568..27538902)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (27817329..27817663)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (27549889..27550223)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene interleukin 21 receptor Neighboring gene uncharacterized LOC124903668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27460829-27461706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10632 Neighboring gene IL21R antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27482643-27483144 Neighboring gene general transcription factor IIIC subunit 1 Neighboring gene MPRA-validated peak2546 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10634 Neighboring gene katanin interacting protein Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:27644974-27645660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27648141-27648641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27652441-27653082 Neighboring gene uncharacterized LOC107984874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27711973-27712473 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:27713579-27714080 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:27714081-27714580 Neighboring gene uncharacterized LOC100128079

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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 15498
  • Sharpr-MPRA regulatory region 5680

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_074826.1 

    Range
    101..435
    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
    27538568..27538902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    27817329..27817663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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