U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129999990 ATAC-STARR-seq lymphoblastoid silent region 18998 [ Homo sapiens (human) ]

Gene ID: 129999990, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129999990
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18998
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 LOC129999990 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (22589086..22589235)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (22863021..22863108)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (22446599..22446748)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 3 catalytic subunit gamma Neighboring gene uncharacterized LOC124901905 Neighboring gene BTF3 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22406579-22407079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22408405-22409369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22409593-22410470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22410471-22411346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22413914-22414436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18990 Neighboring gene Sharpr-MPRA regulatory region 12029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22421349-22422242 Neighboring gene sorbin and SH3 domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22429393-22430084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22430085-22430775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22431841-22432559 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22435755-22436448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22439222-22439914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22442189-22442858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22447071-22448071 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22454615-22455362 Neighboring gene PDZ and LIM domain 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22455363-22456110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22458799-22459676 Neighboring gene uncharacterized LOC107986876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27082 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:22462104-22462604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19003 Neighboring gene chromosome 8 open reading frame 58 Neighboring gene cell cycle and apoptosis regulator 2 Neighboring gene bridging integrator 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 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_179436.1 

    Range
    101..250
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    22589086..22589235
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    22863021..22863108
    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