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LOC130001879 ATAC-STARR-seq lymphoblastoid silent region 19945 [ Homo sapiens (human) ]

Gene ID: 130001879, updated on 12-Sep-2024

Summary

Gene symbol
LOC130001879
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19945
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 LOC130001879 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 (71910717..71910956)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (84061067..84061306)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (74525633..74525872)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:74304891-74306090 Neighboring gene cell migration inducing hyaluronidase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:74358750-74359614 Neighboring gene NANOG hESC enhancer GRCh37_chr9:74368830-74369517 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74371765-74372408 Neighboring gene HNF1 motif-containing MPRA enhancer 224 Neighboring gene hESC enhancers GRCh37_chr9:74383087-74383768 and GRCh37_chr9:74383769-74384450 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:74408684-74409233 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:74409234-74409782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28454 Neighboring gene glucosamine-6-phosphate deaminase 2 pseudogene Neighboring gene abhydrolase domain containing 17B, depalmitoylase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28457 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74534388-74534894 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74535401-74535906 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:74535907-74536412 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:74536413-74536918 Neighboring gene chromosome 9 open reading frame 85 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74568411-74569057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74578682-74579426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74579427-74580171 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:74604827-74606026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:74622307-74622838 Neighboring gene heat shock protein family B (small) member 1 pseudogene 1

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_181325.1 

    Range
    101..340
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    71910717..71910956
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    84061067..84061306
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    GenBank, FASTA, Sequence Viewer (Graphics)