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LOC130068844 ATAC-STARR-seq lymphoblastoid silent region 21077 [ Homo sapiens (human) ]

Gene ID: 130068844, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130068844
Gene description
ATAC-STARR-seq lymphoblastoid silent region 21077
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]
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Genomic context

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See LOC130068844 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153971899..153972138)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152245619..152245858)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153237350..153237589)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153200750-153201255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153201256-153201760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153204898-153205662 Neighboring gene renin binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153210247-153211010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153213176-153213715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30044 Neighboring gene host cell factor C1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153231131-153231789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153231790-153232449 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153234675-153234853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153235869-153236718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21078 Neighboring gene HCFC1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21079 Neighboring gene transmembrane protein 187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30048 Neighboring gene microRNA 3202-1 Neighboring gene microRNA 3202-2 Neighboring gene CRISPRi-validated cis-regulatory element chrX.2695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153265676-153266176 Neighboring gene NFE2L2 motif-containing MPRA enhancer 190/191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153277410-153278394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153278395-153279378 Neighboring gene interleukin 1 receptor associated kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153285318-153286287

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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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_203258.1 

    Range
    101..340
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    153971899..153972138
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152245619..152245858
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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