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LOC121331296 Sharpr-MPRA regulatory region 13363 [ Homo sapiens (human) ]

Gene ID: 121331296, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121331296
Gene description
Sharpr-MPRA regulatory region 13363
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This region also displayed repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (27426212..27426506)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (27703030..27703324)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (27283729..27284023)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27093978-27094478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27094479-27094979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:27099673-27100624 Neighboring gene stathmin 4 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:27132319-27132821 Neighboring gene tripartite motif containing 35 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27183969-27184798 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:27184956-27185152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27139 Neighboring gene protein tyrosine kinase 2 beta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19048 Neighboring gene Sharpr-MPRA regulatory region 9089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27141 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:27219644-27220174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27287852-27288568 Neighboring gene microRNA 6842 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:27316840-27317083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27319910-27320838 Neighboring gene cholinergic receptor nicotinic alpha 2 subunit

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_074320.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    27426212..27426506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    27703030..27703324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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