U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121967058 Sharpr-MPRA regulatory region 5603 [ Homo sapiens (human) ]

Gene ID: 121967058, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121967058
Gene description
Sharpr-MPRA regulatory region 5603
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jul 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (6343489..6343783)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (5869131..5869425)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (6403549..6403843)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6304377-6304934 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6305171-6305522 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6309743-6310284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 150 Neighboring gene G protein-coupled receptor 153 Neighboring gene hes family bHLH transcription factor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6329739-6330330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6330331-6330921 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6333683-6333849 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6335064-6335654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6339577-6340442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6340686-6341235 Neighboring gene acyl-CoA thioesterase 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 76 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:6361272-6362471 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6396158-6396892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6397980-6398642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6398643-6399303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6399966-6400626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6417160-6418127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 77 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 78 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 79 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 80 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6424607-6425106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6427779-6428559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6434479-6434978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6445825-6446810 Neighboring gene H3K27ac hESC enhancers GRCh37_chr1:6453176-6453687 and GRCh37_chr1:6453688-6454200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:6454201-6454711 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6455464-6455988 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:6474153-6474654 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:6474655-6475154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6483551-6484165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6484166-6484779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 82 Neighboring gene hes family bHLH transcription factor 2 Neighboring gene microRNA 4252 Neighboring gene espin

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_076198.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    6343489..6343783
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    5869131..5869425
    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