U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130003802 ATAC-STARR-seq lymphoblastoid silent region 2362 [ Homo sapiens (human) ]

Gene ID: 130003802, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130003802
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2362
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 represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC130003802 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (49398104..49398263)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (50246889..50247048)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (50606150..50606309)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene C10orf71 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:50505091-50505268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2361 Neighboring gene chromosome 10 open reading frame 71 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:50543527-50544726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50587592-50588092 Neighboring gene dorsal root ganglia homeobox Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 17 Neighboring gene ERCC excision repair 6, chromatin remodeling factor Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:50679962-50681161 Neighboring gene piggyBac transposable element derived 3

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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_183248.1 

    Range
    101..260
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    49398104..49398263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    50246889..50247048
    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