U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC124049160 Sharpr-MPRA regulatory region 1187 [ Homo sapiens (human) ]

Gene ID: 124049160, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC124049160
Gene description
Sharpr-MPRA regulatory region 1187
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 15:Elon, transcription elongation, stronger H3K36me3, more exonic) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Feb 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC124049160 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (8868479..8868773)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (10875368..10875662, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (8725989..8726283)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379225 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8559273-8560240 Neighboring gene claudin 23 Neighboring gene NANOG hESC enhancer GRCh37_chr8:8594010-8594511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26976 Neighboring gene MPRA-validated peak6897 silencer Neighboring gene multifunctional ROCO family signaling regulator 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8679219-8679761 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26979 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8741828-8742802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8747640-8748600 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8748601-8749560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8749561-8750521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18903 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18904 Neighboring gene RNA, U6 small nuclear 682, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:8771372-8771981 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:8774498-8774763 Neighboring gene MRPS18C pseudogene 2

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_078489.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    8868479..8868773
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    4483213..4483507 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    10875368..10875662 complement
    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