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LOC129992634 ATAC-STARR-seq lymphoblastoid silent region 15455 [ Homo sapiens (human) ]

Gene ID: 129992634, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992634
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15455
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 LOC129992634 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (56821543..56821802)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (60309455..60309714)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (57687709..57687968)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15454 Neighboring gene RNA, 7SL, cytoplasmic 357, pseudogene Neighboring gene serine peptidase inhibitor Kazal type 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57710833-57711338 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57711339-57711844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:57714899-57715398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21585 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57773523-57774452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15457 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:57775383-57776312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:57780934-57781434 Neighboring gene RE1 silencing transcription factor Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:57802865-57804064 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:57831417-57831519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21587 Neighboring gene nitric oxide associated 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_172080.1 

    Range
    101..360
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    56821543..56821802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    60309455..60309714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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