U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129994554 ATAC-STARR-seq lymphoblastoid active region 23059 [ Homo sapiens (human) ]

Gene ID: 129994554, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC129994554
Gene description
ATAC-STARR-seq lymphoblastoid active region 23059
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC129994554 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (131758208..131758257)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132278198..132278247)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Rap guanine nucleotide exchange factor 6 Neighboring gene Sharpr-MPRA regulatory region 5338 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:130970112-130970694 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:130970824-130972023 Neighboring gene folliculin interacting protein 1 Neighboring gene ACTB pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16309 Neighboring gene meiotic kinetochore factor Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:131267911-131268464 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131293433-131293633 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131329699-131330242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131330787-131331330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131337447-131338042 Neighboring gene acyl-CoA synthetase long chain family member 6 Neighboring gene ACSL6 antisense RNA 1

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_174000.1 

    Range
    101..150
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    131758208..131758257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    132278198..132278247
    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