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LOC130008328 ATAC-STARR-seq lymphoblastoid silent region 4681 [ Homo sapiens (human) ]

Gene ID: 130008328, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008328
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4681
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 LOC130008328 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (79689672..79690191)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (79668328..79668847)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (80083452..80083971)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene synaptotagmin 1 Neighboring gene microRNA 1252 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79906476-79906976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79906977-79907477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:79926619-79927119 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79933315-79933826 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79933827-79934340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79936391-79936902 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79938953-79939466 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79941058-79941786 Neighboring gene NOP56 ribonucleoprotein pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:80048601-80049285 Neighboring gene PPP1R12A antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4682 Neighboring gene pro-apoptotic WT1 regulator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:80104382-80104890 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:80177965-80178557 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:80178558-80179149 Neighboring gene uncharacterized LOC124902974 Neighboring gene protein phosphatase 1 regulatory subunit 12A Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:80268321-80268858 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:80268859-80269395 Neighboring gene RNA, 5S ribosomal pseudogene 363

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_186897.1 

    Range
    101..620
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    79689672..79690191
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    79668328..79668847
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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