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LOC130061897 ATAC-STARR-seq lymphoblastoid silent region 9099 [ Homo sapiens (human) ]

Gene ID: 130061897, updated on 12-Sep-2024

Summary

Gene symbol
LOC130061897
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9099
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 LOC130061897 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80101128..80101747)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (81001567..81002186)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78074927..78075546)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene coiled-coil domain 40 molecular ruler complex subunit Neighboring gene uncharacterized LOC124904074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78039691-78040515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78056255-78056756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78064021-78064580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12928 Neighboring gene microRNA 1268b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78083610-78084585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78086615-78087127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78091523-78092024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78097302-78097924 Neighboring gene alpha glucosidase Neighboring gene ReSE screen-validated silencer GRCh37_chr17:78107357-78107522 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:78120154-78120868 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:78120869-78121581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78121582-78122295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78122296-78123008 Neighboring gene eukaryotic translation initiation factor 4A3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:78126203-78126704 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:78126705-78127204 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:78129355-78129892 Neighboring gene Sharpr-MPRA regulatory region 5287 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:78151904-78153103 Neighboring gene caspase recruitment domain family member 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78163065-78163581 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:78178385-78179584 Neighboring gene N-sulfoglucosamine sulfohydrolase

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_196998.1 

    Range
    101..720
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    80101128..80101747
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791802.1 Reference GRCh38.p14 PATCHES

    Range
    125834..126453
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    81001567..81002186
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    GenBank, FASTA, Sequence Viewer (Graphics)