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LOC130068865 ATAC-STARR-seq lymphoblastoid silent region 21099 [ Homo sapiens (human) ]

Gene ID: 130068865, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130068865
Gene description
ATAC-STARR-seq lymphoblastoid silent region 21099
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 LOC130068865 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154397420..154397599)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152633940..152634119)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153625761..153625940)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Xq28 proximal FLNA-EMD recombination region Neighboring gene filamin A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153596747-153597274 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153597275-153597800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21087 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153599383-153599908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153599914-153600555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21098 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153608033-153608612 Neighboring gene Xq28 distal FLNA-EMD recombination region Neighboring gene emerin Neighboring gene uncharacterized LOC124905228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21100 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153626083-153626628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30060 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153627173-153627718 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153627719-153628262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153628263-153628808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153628809-153629352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30061 Neighboring gene deoxyribonuclease 1 like 1 Neighboring gene small nucleolar RNA, H/ACA box 70 Neighboring gene ribosomal protein L10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21101 Neighboring gene tafazzin, phospholipid-lysophospholipid transacylase

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_203279.1 

    Range
    101..280
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154397420..154397599
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152633940..152634119
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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