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LOC130055655 ATAC-STARR-seq lymphoblastoid silent region 5751 [ Homo sapiens (human) ]

Gene ID: 130055655, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130055655
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5751
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 LOC130055655 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (52950819..52951028)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (47158759..47158968)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (53417537..53417746)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8397 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr14:53257919-53258432 and GRCh37_chr14:53258433-53258947 Neighboring gene uncharacterized LOC105370500 Neighboring gene COP9 signalosome subunit 9 pseudogene Neighboring gene glucosamine-phosphate N-acetyltransferase 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:53301633-53302238 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:53302239-53302843 Neighboring gene Sharpr-MPRA regulatory region 8176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:53350617-53351142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:53351143-53351668 Neighboring gene FERM domain containing kindlin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8398 Neighboring gene Sharpr-MPRA regulatory region 10339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:53418467-53419045 Neighboring gene NADH:ubiquinone oxidoreductase subunit B3 pseudogene 3 Neighboring gene DDHD domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5752

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_190076.1 

    Range
    101..310
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    52950819..52951028
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    47158759..47158968
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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