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LOC112840935 Sharpr-MPRA regulatory region 13975 [ Homo sapiens (human) ]

Gene ID: 112840935, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112840935
Gene description
Sharpr-MPRA regulatory region 13975
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 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (43676370..43676664)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (43681740..43682034)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (43903509..43903803)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene THADA armadillo repeat containing Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15673 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:43653235-43654434 Neighboring gene RNA, U6 small nuclear 958, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15679 Neighboring gene RNA, 7SL, cytoplasmic 531, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43809645-43809864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11427 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43892733-43893363 Neighboring gene pleckstrin homology, MyTH4 and FERM domain containing H2 Neighboring gene zinc finger protein 106 homolog (mouse) pseudogene Neighboring gene C1GALT1 specific chaperone 1 like Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43942164-43942363 Neighboring gene MPRA-validated peak3684 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43973372-43973613 Neighboring gene RN7SK pseudogene 66

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_061302.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    43676370..43676664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    43681740..43682034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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