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LOC129993644 ATAC-STARR-seq lymphoblastoid silent region 15912 [ Homo sapiens (human) ]

Gene ID: 129993644, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993644
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15912
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 LOC129993644 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (10111632..10111731)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (10050933..10051032)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (10111744..10111843)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944391-9944892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944893-9945392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15911 Neighboring gene uncharacterized LOC124900939 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10101715-10102617 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10102618-10103520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:10108167-10108948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10127135-10127785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10140102-10140735 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:10157229-10157880 Neighboring gene ATP synthase c subunit lysine N-methyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15916 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:10251320-10251542 Neighboring gene chaperonin containing TCP1 subunit 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_173090.1 

    Range
    101..200
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    10111632..10111731
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    10050933..10051032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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