U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130064384 ATAC-STARR-seq lymphoblastoid silent region 10589 [ Homo sapiens (human) ]

Gene ID: 130064384, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130064384
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10589
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 LOC130064384 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (38878062..38878111)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41682118..41682167)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (39368702..39368751)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak3474 silencer Neighboring gene uncharacterized LOC124904712 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr19:39314813-39315370 Neighboring gene enoyl-CoA hydratase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39333551-39334051 Neighboring gene heterogeneous nuclear ribonucleoprotein L Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39338887-39339825 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39339826-39340763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39343185-39343829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10587 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:39350790-39350958 Neighboring gene Sharpr-MPRA regulatory region 3140 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39356343-39356918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39360061-39360631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39360661-39361267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39361268-39361873 Neighboring gene Ras and Rab interactor like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14603 Neighboring gene sirtuin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39384205-39384706 Neighboring gene NFKB inhibitor beta

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 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_198801.1 

    Range
    101..150
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    38878062..38878111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_014040929.1 Reference GRCh38.p14 PATCHES

    Range
    287734..287783
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    41682118..41682167
    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