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LOC121587552 Sharpr-MPRA regulatory region 4304 [ Homo sapiens (human) ]

Gene ID: 121587552, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587552
Gene description
Sharpr-MPRA regulatory region 4304
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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (69529626..69529920)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75331862..75332156)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (69563529..69563823)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 111 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr16:69477408-69477690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11039 Neighboring gene cytochrome b5 type B Neighboring gene ReSE screen-validated silencer GRCh37_chr16:69488879-69489096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11041 Neighboring gene uncharacterized LOC105371325 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:69556814-69558013 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:69563811-69565010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69597937-69598833 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:69599594-69599770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7664 Neighboring gene microRNA 1538 Neighboring gene nuclear factor of activated T cells 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11043 Neighboring gene MPRA-validated peak2631 silencer

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_074839.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    69529626..69529920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    75331862..75332156
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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