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LOC130004589 ATAC-STARR-seq lymphoblastoid silent region 2751 [ Homo sapiens (human) ]

Gene ID: 130004589, updated on 12-Sep-2024

Summary

Gene symbol
LOC130004589
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2751
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

See LOC130004589 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (102226281..102226330)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (103111268..103111317)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (103986038..103986087)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2745 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103880011-103880762 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:103880763-103881514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:103881515-103882264 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103887116-103887946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3922 Neighboring gene LIM domain binding 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2750 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103897995-103899194 Neighboring gene PPARG related coactivator 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103911632-103912831 Neighboring gene nucleolar and coiled-body phosphoprotein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:103989615-103989783 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3925 Neighboring gene ELOVL fatty acid elongase 3 Neighboring gene paired like homeodomain 3 Neighboring gene golgi brefeldin A resistant guanine nucleotide exchange factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104029238-104029738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104029739-104030239 Neighboring gene Sharpr-MPRA regulatory region 13217 Neighboring gene Sharpr-MPRA regulatory region 15234 Neighboring gene uncharacterized LOC107984263

Genomic regions, transcripts, and products

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_184034.1 

    Range
    101..150
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    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    102226281..102226330
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    103111268..103111317
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)