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LOC130067122 ATAC-STARR-seq lymphoblastoid silent region 13554 [ Homo sapiens (human) ]

Gene ID: 130067122, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130067122
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13554
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 LOC130067122 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (24554887..24555246)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (25016494..25016853)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene SPECC1L-ADORA2A readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24825428-24826389 Neighboring gene ADORA2A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24829365-24829914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24831043-24831543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13551 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24840685-24840876 Neighboring gene adenosine A2a receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18773 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24875502-24875689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24901494-24902032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24902033-24902569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18776 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24905414-24905687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18778 Neighboring gene beta-ureidopropionase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24957881-24958382 Neighboring gene guanylyl cyclase domain containing 1 Neighboring gene uncharacterized LOC124905091 Neighboring gene small nuclear ribonucleoprotein D3 polypeptide

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

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_201537.1 

    Range
    101..460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    24554887..24555246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    25016494..25016853
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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