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LOC129933482 ATAC-STARR-seq lymphoblastoid silent region 11352 [ Homo sapiens (human) ]

Gene ID: 129933482, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933482
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11352
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 LOC129933482 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (36966217..36967026)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (36973355..36974164)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (37193360..37194169)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905990 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:36964254-36964949 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:36981017-36981669 Neighboring gene vitrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15577 Neighboring gene Sharpr-MPRA regulatory region 5815 Neighboring gene RNA, U6 small nuclear 577, pseudogene Neighboring gene striatin Neighboring gene MPRA-validated peak3656 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr2:37189639-37189834 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:37230067-37230233 Neighboring gene HEAT repeat containing 5B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15579 Neighboring gene G-patch domain containing 11 Neighboring gene eukaryotic translation initiation factor 2 alpha kinase 2

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_166508.1 

    Range
    101..910
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    36966217..36967026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    36973355..36974164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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