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LOC112935957 Sharpr-MPRA regulatory region 11074 [ Homo sapiens (human) ]

Gene ID: 112935957, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935957
Gene description
Sharpr-MPRA regulatory region 11074
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). It also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112935957 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 (72462718..72463012)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (72504676..72504970)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (72511869..72512163)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72367959-72368500 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:72384094-72384660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14527 Neighboring gene MPRA-validated peak4695 silencer Neighboring gene RING1 and YY1 binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14529 Neighboring gene uncharacterized LOC105377160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72531660-72532160 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72536327-72536844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72536845-72537362 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:72539260-72539964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72541478-72541982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20088 Neighboring gene NANOG hESC enhancer GRCh37_chr3:72585386-72586027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20089 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:72604422-72604612 Neighboring gene uncharacterized LOC124909394 Neighboring gene small nucleolar RNA U13

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_061472.1 

    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
    72462718..72463012
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332691.1 Reference GRCh38.p14 PATCHES

    Range
    137657..137951
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    72504676..72504970
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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