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LOC112806060 ReSE screen-validated silencer GRCh37_chr2:174904545-174904945 [ Homo sapiens (human) ]

Gene ID: 112806060, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112806060
Gene description
ReSE screen-validated silencer GRCh37_chr2:174904545-174904945
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 represents an accessible chromatin region used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. It was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. A subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Apr 2023]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (174039817..174040217)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (174526174..174526574)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (174904649..174904943)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sp3 transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16769 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:174827792-174828615 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:174828616-174829438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12121 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:174857477-174857650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16770 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:174888471-174889670 Neighboring gene long intergenic non-protein coding RNA 1960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:174901892-174902392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:174902393-174902893 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:174914257-174914460 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:174916218-174917417 Neighboring gene ribosomal protein SA pseudogene 24 Neighboring gene uncharacterized LOC105373746

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 8299

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_060913.2 

    Range
    101..501
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    174039817..174040217
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    174526174..174526574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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