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LOC122094898 Sharpr-MPRA regulatory region 6417 [ Homo sapiens (human) ]

Gene ID: 122094898, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122094898
Gene description
Sharpr-MPRA regulatory region 6417
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element 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 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (112444287..112444581)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (112456523..112456817)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (112986909..112987203)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:112928422-112928957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:112928958-112929492 Neighboring gene thioredoxin pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1195 Neighboring gene CTTNBP2 N-terminal like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:112947097-112947622 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:112950375-112950562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1512 Neighboring gene MPRA-validated peak369 silencer Neighboring gene microRNA 4256 Neighboring gene Wnt family member 2B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:113050855-113051398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1200 Neighboring gene Sharpr-MPRA regulatory region 8072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:113052323-113052822 Neighboring gene suppression of tumorigenicity 7 like

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_076412.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    112444287..112444581
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    112456523..112456817
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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