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LOC129660237 ReSE screen-validated silencer GRCh37_chr1:43424712-43424895 [ Homo sapiens (human) ]

Gene ID: 129660237, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129660237
Gene description
ReSE screen-validated silencer GRCh37_chr1:43424712-43424895
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 includes an accessible chromatin region used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. A subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. This locus also includes an accessible chromatin subregion 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 LOC129660237 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 (42958759..42959224)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (42829229..42829694)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (43424430..43424895)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATPase H+ transporting V1 subunit E1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43392725-43393224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43394256-43394898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43394899-43395539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 902 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43400317-43401109 Neighboring gene solute carrier family 2 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43406478-43406986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43408512-43409020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43411987-43412488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43412489-43412988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43416007-43416542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 909 Neighboring gene Sharpr-MPRA regulatory region 3978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43418797-43419741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 910 Neighboring gene ATPase H+ transporting V0 subunit c pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 772 Neighboring gene Sharpr-MPRA regulatory region 619 Neighboring gene SLC2A1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43436637-43437138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43437139-43437638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43438752-43439252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43439253-43439753 Neighboring gene RNA, U6 small nuclear 880, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43473322-43474029 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43474030-43474738 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:43474739-43475446 Neighboring gene uncharacterized LOC124904715

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 773

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_157275.2 

    Range
    101..566
    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
    42958759..42959224
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    42829229..42829694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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