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LOC130005814 ATAC-STARR-seq lymphoblastoid silent region 3408 [ Homo sapiens (human) ]

Gene ID: 130005814, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005814
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3408
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

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See LOC130005814 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61899019..61899068)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61887823..61887872)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61666491..61666540)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene fatty acid desaturase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61615549-61616049 Neighboring gene uncharacterized LOC124902679 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61624465-61624966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61628720-61629220 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61629221-61629721 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:61642149-61642697 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61646639-61647348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61655245-61655746 Neighboring gene fatty acid desaturase 3 Neighboring gene microRNA 6746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61657348-61658037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61658038-61658726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61666908-61667879 Neighboring gene RAB3A interacting protein like 1 Neighboring gene Sharpr-MPRA regulatory region 8487 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:61705992-61706140 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:61709325-61709979 Neighboring gene RNA, U6 small nuclear 1243, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61711149-61711650 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:61713521-61713684 Neighboring gene uncharacterized LOC107984334 Neighboring gene bestrophin 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

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_185259.1 

    Range
    101..150
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    61899019..61899068
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    61887823..61887872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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