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LOC129619399 ReSE screen-validated silencer GRCh37_chrX:389565-389736 [ Homo sapiens (human) ]

Gene ID: 129619399, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129619399
Gene description
ReSE screen-validated silencer GRCh37_chrX:389565-389736
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 region is found within pseudoautosomal region 1 (PAR1) of chromosomes X and Y, where each chromosome contains the same DNA region. This genomic sequence represents 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. This region was identified as a functional silencer in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
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Genomic context

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See LOC129619399 in Genome Data Viewer
Location:
X;Y
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (428830..429001)
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (428830..429001)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (260587..260758)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (268120..268291)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (389565..389736)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (339565..339736)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 685 Neighboring gene protein phosphatase 2 regulatory subunit B''beta Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:323668-324173 and GRCh37_chrY:273658-274173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:274174-274688 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:333708-333890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:335885-336775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:357819-358704 Neighboring gene uncharacterized LOC102724521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:396687-397186 Neighboring gene OCT4-NANOG hESC enhancers GRCh37_chrX:406609-407442 and GRCh37_chrY:356916-357447 Neighboring gene CNE-5 enhancer upstream of SHOX Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:461079-461645 Neighboring gene CNE-3 enhancer upstream of SHOX Neighboring gene fatty acid binding protein 5 pseudogene 13

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 685 Neighboring gene protein phosphatase 2 regulatory subunit B''beta Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:323668-324173 and GRCh37_chrY:273658-274173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:274174-274688 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:333708-333890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:335885-336775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:357819-358704 Neighboring gene uncharacterized LOC102724521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:396687-397186 Neighboring gene OCT4-NANOG hESC enhancers GRCh37_chrX:406609-407442 and GRCh37_chrY:356916-357447 Neighboring gene CNE-5 enhancer upstream of SHOX Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:461079-461645 Neighboring gene CNE-3 enhancer upstream of SHOX Neighboring gene fatty acid binding protein 5 pseudogene 13

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

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)

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_157074.1 

    Range
    101..272
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    428830..429001
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    428830..429001
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187634.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    112183..112354
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187667.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    101323..101494
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    260587..260758
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    268120..268291
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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