U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123493220 Sharpr-MPRA regulatory region 1071 [ Homo sapiens (human) ]

Gene ID: 123493220, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123493220
Gene description
Sharpr-MPRA regulatory region 1071
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Nov 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC123493220 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (152930357..152930651)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (156253558..156253852)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (153851509..153851803)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:153729642-153730323 Neighboring gene ADP ribosylation factor interacting protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:153755875-153756375 Neighboring gene NSA2 pseudogene 6 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:153764305-153765504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153768357-153768857 Neighboring gene Sharpr-MPRA regulatory region 8200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15754 Neighboring gene Sharpr-MPRA regulatory region 8192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153877563-153878382 Neighboring gene uncharacterized LOC729870 Neighboring gene family with sequence similarity 192, member A pseudogene Neighboring gene FH2 domain containing 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:153892920-153894119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153894208-153894728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153894729-153895248 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:153912200-153913399 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:153913429-153913928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153942327-153943122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153944769-153945310 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:153949611-153950259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154028483-154028983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154033423-154033922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154057659-154058160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15755 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154127146-154128051 Neighboring gene tripartite motif containing 2 Neighboring gene NANOG hESC enhancer GRCh37_chr4:154130352-154131177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154143059-154143560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154159939-154160440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154160441-154160940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154162218-154162718 Neighboring gene uncharacterized LOC105377496

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_077644.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    152930357..152930651
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    156253558..156253852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases