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LOC130007028 ATAC-STARR-seq lymphoblastoid silent region 4049 [ Homo sapiens (human) ]

Gene ID: 130007028, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007028
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4049
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 LOC130007028 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (126304018..126304147)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (126335445..126335574)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (126173913..126174042)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126152727-126153534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:126162703-126163207 Neighboring gene TIR domain containing adaptor protein Neighboring gene TIRAP antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5708 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:126185709-126185914 Neighboring gene decapping enzyme, scavenger Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126197556-126198280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126198281-126199003 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:126203043-126203544 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:126204673-126205174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126206322-126206884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126206885-126207448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126207449-126208010 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:126208933-126210132 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:126224473-126225216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126225217-126225958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126225959-126226702 Neighboring gene G-quadruplex forming sequence containing lncRNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:126228189-126228930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:126234481-126234998 Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:126263623-126264550

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_186472.1 

    Range
    101..230
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    126304018..126304147
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    126335445..126335574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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