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LOC130064461 ATAC-STARR-seq lymphoblastoid silent region 10628 [ Homo sapiens (human) ]

Gene ID: 130064461, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064461
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10628
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 LOC130064461 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 (40444267..40444586)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (43264926..43265245)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (40950174..40950493)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40915393-40915986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40915987-40916578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40920095-40920743 Neighboring gene periaxin Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:40926600-40927100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:40930422-40931224 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40939147-40939975 Neighboring gene SERTA domain containing 1 Neighboring gene CRISPRi-validated cis-regulatory element chr19.4185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10629 Neighboring gene SERTAD3 antisense RNA 1 Neighboring gene SERTA domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14655 Neighboring gene biliverdin reductase B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10630 Neighboring gene spectrin beta, non-erythrocytic 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:41029231-41029526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10633

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_198878.1 

    Range
    101..420
    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
    40444267..40444586
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    43264926..43265245
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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