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LOC130060027 ATAC-STARR-seq lymphoblastoid silent region 8041 [ Homo sapiens (human) ]

Gene ID: 130060027, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060027
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8041
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 LOC130060027 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (4498954..4499003)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4388845..4388894)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4402249..4402298)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SPNS lysolipid transporter 3, sphingosine-1-phosphate (putative) Neighboring gene uncharacterized LOC124903899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4384268-4385023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11541 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4392946-4394145 Neighboring gene SPNS2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4402340-4402975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4402976-4403610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4405882-4406398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4406399-4406914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4407104-4407604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4407605-4408105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4408166-4408835 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4408836-4409504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11542 Neighboring gene SPNS lysolipid transporter 2, sphingosine-1-phosphate Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4415494-4416140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4417497-4418154 Neighboring gene MYB binding protein 1a Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11543 Neighboring gene gamma-glutamyltransferase 6

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_194448.1 

    Range
    101..150
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    4498954..4499003
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4388845..4388894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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