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LOC113174997 Sharpr-MPRA regulatory region 3623 [ Homo sapiens (human) ]

Gene ID: 113174997, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113174997
Gene description
Sharpr-MPRA regulatory region 3623
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Sep 2018]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (37314833..37315127)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (37138406..37138700)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (37282609..37282903)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37137173-37137771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17131 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:37139693-37140286 Neighboring gene CRISPR perturbation-validated PIM1 cis-regulatory element TAD2.SE2.HS2 Neighboring gene Pim-1 proto-oncogene, serine/threonine kinase Neighboring gene Sharpr-MPRA regulatory region 1580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17134 Neighboring gene transmembrane protein 217B Neighboring gene transmembrane protein 217 Neighboring gene Sharpr-MPRA regulatory region 10381 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24455 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:37225915-37226550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37232157-37232657 Neighboring gene TBC1 domain family member 22B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17138 Neighboring gene uncharacterized LOC105375040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24457 Neighboring gene RNA, 7SL, cytoplasmic 273, pseudogene Neighboring gene ring finger protein 8

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_061675.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    37314833..37315127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    37138406..37138700
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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