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LOC130003001 ATAC-STARR-seq lymphoblastoid silent region 20509 [ Homo sapiens (human) ]

Gene ID: 130003001, updated on 12-Sep-2024

Summary

Gene symbol
LOC130003001
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20509
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 LOC130003001 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 (136363480..136363979)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148592811..148593310)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139257932..139258431)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC26102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139218370-139218998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139218999-139219627 Neighboring gene Sharpr-MPRA regulatory region 1004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139222157-139222686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139222687-139223215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139227274-139227906 Neighboring gene G protein signaling modulator 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139237289-139238070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139238071-139238852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139239387-139240040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139240041-139240694 Neighboring gene Sharpr-MPRA regulatory region 3186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20508 Neighboring gene uncharacterized LOC124902309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139258773-139259663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139259664-139260553 Neighboring gene DNL-type zinc finger Neighboring gene caspase recruitment domain family member 9 Neighboring gene Sharpr-MPRA regulatory region 3996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139268303-139269016 Neighboring gene small nuclear RNA activating complex polypeptide 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139291906-139293105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139294835-139295771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139301375-139301963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20515 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20516 Neighboring gene endosome associated trafficking regulator 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_182447.1 

    Range
    101..600
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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
    136363480..136363979
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148592811..148593310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)