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LOC130006004 ATAC-STARR-seq lymphoblastoid active region 4953 [ Homo sapiens (human) ]

Gene ID: 130006004, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006004
Gene description
ATAC-STARR-seq lymphoblastoid active region 4953
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 LOC130006004 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 (65334104..65334153)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65327422..65327471)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65101575..65101624)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3515 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65086579-65086802 Neighboring gene CDC42 effector protein 2 Neighboring gene uncharacterized LOC124902691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65104413-65104913 Neighboring gene double PHD fingers 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3518 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3521 Neighboring gene Sharpr-MPRA regulatory region 3865 Neighboring gene tigger transposable element derived 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65144096-65144596 Neighboring gene FERM domain containing 8 Neighboring gene solute carrier family 25 member 45 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:65149420-65150619 Neighboring gene Sharpr-MPRA regulatory region 10780

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_185449.1 

    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
    65334104..65334153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65327422..65327471
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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