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LOC129929403 ATAC-STARR-seq lymphoblastoid silent region 265 [ Homo sapiens (human) ]

Gene ID: 129929403, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929403
Gene description
ATAC-STARR-seq lymphoblastoid silent region 265
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 LOC129929403 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (11654379..11654518)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (11198431..11198570)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11714436..11714575)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11561504-11562071 Neighboring gene dispatched RND transporter family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11575295-11575922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11619527-11620028 Neighboring gene Sharpr-MPRA regulatory region 3841 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:11640244-11640440 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:11660896-11661396 Neighboring gene long intergenic non-protein coding RNA 1647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11709789-11710497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11710498-11711205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 266 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:11718034-11719233 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 169 Neighboring gene F-box protein 2 Neighboring gene F-box protein 44 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11743170-11743751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11744701-11745201 Neighboring gene F-box protein 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:11750065-11750574 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:11750575-11751082 Neighboring gene mitotic arrest deficient 2 like 2 Neighboring gene dorsal inhibitory axon guidance protein

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_162460.1 

    Range
    101..240
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    11654379..11654518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    11198431..11198570
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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