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LOC112935934 Sharpr-MPRA regulatory region 4350 [ Homo sapiens (human) ]

Gene ID: 112935934, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935934
Gene description
Sharpr-MPRA regulatory region 4350
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 non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112935934 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (41026578..41026872)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (41041934..41042228)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (41068069..41068363)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377043 Neighboring gene MPRA-validated peak4616 silencer Neighboring gene ribosomal protein S27 pseudogene 4 Neighboring gene NANOG hESC enhancer GRCh37_chr3:40885161-40886029 Neighboring gene uncharacterized LOC124906230 Neighboring gene NANOG hESC enhancer GRCh37_chr3:40912794-40913474 Neighboring gene NANOG hESC enhancer GRCh37_chr3:40961458-40962007 Neighboring gene Sharpr-MPRA regulatory region 10975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:41010264-41010764 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:41012603-41013802 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:41037247-41037747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:41039383-41040340 Neighboring gene uncharacterized LOC105377045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19722 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:41137060-41138259 Neighboring gene Sharpr-MPRA regulatory region 10354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19723 Neighboring gene mitochondrial ribosomal protein S31 pseudogene 1

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_061450.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    41026578..41026872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    41041934..41042228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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