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LOC130063409 ATAC-STARR-seq lymphoblastoid silent region 10011 [ Homo sapiens (human) ]

Gene ID: 130063409, updated on 12-Sep-2024

Summary

Gene symbol
LOC130063409
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10011
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 LOC130063409 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (8154090..8154139)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (8155193..8155242)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (8218974..8219023)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene C-C motif chemokine ligand 25 Neighboring gene fibrillin 3 Neighboring gene MPRA-validated peak3327 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8175802-8176302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8180417-8180917 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8183744-8184561 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8185348-8185938 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8185939-8186529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8193691-8194192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8206295-8206796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8208101-8208645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8211691-8212662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8212663-8213633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10012 Neighboring gene Sharpr-MPRA regulatory region 3488 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:8226075-8226576 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:8228221-8229026 Neighboring gene ALG11, alpha-1,2-mannosyltransferase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8260104-8260957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8260958-8261810 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8268618-8269588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8280063-8280564 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8285012-8285518 Neighboring gene ceramide synthase 4 Neighboring gene uncharacterized LOC107985282

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_197826.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    8154090..8154139
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    8155193..8155242
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)