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LOC130006383 ATAC-STARR-seq lymphoblastoid active region 5233 [ Homo sapiens (human) ]

Gene ID: 130006383, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006383
Gene description
ATAC-STARR-seq lymphoblastoid active region 5233
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC130006383 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 (73295357..73295406)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (73224517..73224566)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (73006402..73006451)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:72959838-72961037 Neighboring gene uncharacterized LOC105369382 Neighboring gene olfactory receptor family 8 subfamily R member 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:72975095-72975632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:72981035-72981828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:72981829-72982621 Neighboring gene pyrimidinergic receptor P2Y6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:73000363-73000929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3737 Neighboring gene ARHGEF17 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:73019433-73020310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:73020316-73021136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5234 Neighboring gene Rho guanine nucleotide exchange factor 17 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:73031799-73032452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:73032453-73033105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:73033106-73033758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:73036372-73037023 Neighboring gene Sharpr-MPRA regulatory region 2623 Neighboring gene uncharacterized LOC124902710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:73044313-73045026

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 variants in ClinVar

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_185828.1 

    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
    73295357..73295406
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    73224517..73224566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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