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LOC130058358 ATAC-STARR-seq lymphoblastoid silent region 7142 [ Homo sapiens (human) ]

Gene ID: 130058358, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058358
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7142
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 LOC130058358 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (3879922..3880231)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (3907127..3907436)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (3929923..3930232)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3746221-3746721 Neighboring gene TNF receptor associated protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3763763-3764271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7139 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:3781718-3781878 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3786759-3787446 Neighboring gene CREB binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3872073-3872574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3872575-3873074 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:3909888-3910072 Neighboring gene Sharpr-MPRA regulatory region 6998 Neighboring gene DPPA3 pseudogene 6 Neighboring gene Sharpr-MPRA regulatory region 1734 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7141 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:3930393-3930969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4011545-4012044 Neighboring gene long intergenic non-protein coding RNA 2861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4031926-4032449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4032450-4032972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4037243-4037742 Neighboring gene uncharacterized LOC124903633 Neighboring gene adenylate cyclase 9

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_192779.1 

    Range
    101..410
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    3879922..3880231
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    3907127..3907436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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