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LOC130003505 ATAC-STARR-seq lymphoblastoid silent region 2213 [ Homo sapiens (human) ]

Gene ID: 130003505, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003505
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2213
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 LOC130003505 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (22713724..22713843)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (22732725..22732844)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (23002653..23002772)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902393 Neighboring gene phosphatidylinositol-5-phosphate 4-kinase type 2 alpha Neighboring gene tRNA-Pro (GGG) 1-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3137 Neighboring gene NANOG hESC enhancer GRCh37_chr10:22899474-22900008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:22904391-22904959 Neighboring gene Sharpr-MPRA regulatory region 2326 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:22912555-22913055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3145 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:22979554-22980468 Neighboring gene VISTA enhancer hs2048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2214 Neighboring gene hESC enhancers GRCh37_chr10:23003153-23003761 and GRCh37_chr10:23003762-23004369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3148 Neighboring gene RNA, U6 small nuclear 413, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:23099405-23099995 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:23099996-23100585 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:23113377-23114576 Neighboring gene uncharacterized LOC105376451

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_182951.1 

    Range
    101..220
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    22713724..22713843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    22732725..22732844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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