U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129993643 ATAC-STARR-seq lymphoblastoid silent region 15911 [ Homo sapiens (human) ]

Gene ID: 129993643, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129993643
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15911
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 LOC129993643 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (9949405..9949464)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (9889210..9889269)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (9949517..9949576)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2112 Neighboring gene taste 2 receptor member 1 Neighboring gene uncharacterized LOC105374649 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:9774748-9775340 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:9775483-9776682 Neighboring gene RNA, 5S ribosomal pseudogene 177 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:9832028-9832528 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:9832529-9833029 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:9833753-9834254 Neighboring gene long intergenic non-protein coding RNA 2221 Neighboring gene NANOG hESC enhancer GRCh37_chr5:9895310-9895811 Neighboring gene uncharacterized LOC107986405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944391-9944892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944893-9945392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22351 Neighboring gene uncharacterized LOC124900939 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10101715-10102617 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10102618-10103520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:10108167-10108948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10127135-10127785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10140102-10140735 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:10157229-10157880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15914 Neighboring gene ATP synthase c subunit lysine N-methyltransferase

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_173089.1 

    Range
    101..160
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    9949405..9949464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    9889210..9889269
    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