U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC124416897 Sharpr-MPRA regulatory region 10495 [ Homo sapiens (human) ]

Gene ID: 124416897, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC124416897
Gene description
Sharpr-MPRA regulatory region 10495
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 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 LOC124416897 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (103759371..103759665)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (104646671..104646965)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (105519129..105519423)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene SH3 and PX domains 2A Neighboring gene uncharacterized LOC124902495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105441739-105442519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105451952-105452918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105455468-105456214 Neighboring gene NFE2L2 motif-containing MPRA enhancer 292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105467435-105468414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105468415-105469393 Neighboring gene NANOG hESC enhancer GRCh37_chr10:105482339-105482840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105491951-105492499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105492500-105493047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105505582-105506103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105506520-105507020 Neighboring gene SH3PXD2A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105507021-105507521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105515685-105516342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105516343-105516998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105531100-105532070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105539219-105539718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105544793-105545294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105549545-105550545 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105560029-105560530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2790 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105563531-105564374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105567495-105567996 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105594413-105594969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105594970-105595525 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105667461-105668062 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 10:105668179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105677593-105678238 Neighboring gene STN1 subunit of CST complex Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105686883-105687548 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105688215-105688880 Neighboring gene uncharacterized LOC102724351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2792

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_079112.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    103759371..103759665
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    104646671..104646965
    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.

Other Literature Sources
Molecular Biology Databases