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LOC130002355 ATAC-STARR-seq lymphoblastoid silent region 20177 [ Homo sapiens (human) ]

Gene ID: 130002355, updated on 12-Sep-2024

Summary

Gene symbol
LOC130002355
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20177
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 LOC130002355 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (111483013..111483432)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (123654442..123654861)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (114245293..114245712)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 2 subfamily K member 2 Neighboring gene Ecm29 proteasome adaptor and scaffold Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114161623-114162149 Neighboring gene RNA, 5S ribosomal pseudogene 294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:114233029-114233528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20179 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28793 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:114288123-114288622 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:114292004-114292628 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105867 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105871 Neighboring gene zinc finger protein 483 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105889 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105891 Neighboring gene prostaglandin reductase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114361778-114362350 Neighboring gene leucine rich repeat containing 37 member A5, pseudogene

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_181801.1 

    Range
    101..520
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    111483013..111483432
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    123654442..123654861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)