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LOC130009796 ATAC-STARR-seq lymphoblastoid silent region 5356 [ Homo sapiens (human) ]

Gene ID: 130009796, updated on 12-Sep-2024

Summary

Gene symbol
LOC130009796
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5356
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 LOC130009796 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (50125424..50125633)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (49346006..49346215)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50699560..50699769)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene deleted in lymphocytic leukemia 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7759 Neighboring gene Sharpr-MPRA regulatory region 84 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5353 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50656434-50657229 Neighboring gene microRNA 15a Neighboring gene NANOG hESC enhancer GRCh37_chr13:50695956-50696481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:50699798-50700508 Neighboring gene ribosomal protein L18 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5359 Neighboring gene deleted in lymphocytic leukemia 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:50715020-50715693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7760 Neighboring gene ST13, Hsp70 interacting protein pseudogene 4 Neighboring gene uncharacterized LOC124900337

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_189336.1 

    Range
    101..310
    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    50125424..50125633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    49346006..49346215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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