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LOC129662940 ReSE screen-validated silencer GRCh37_chr11:61197385-61197720 [ Homo sapiens (human) ]

Gene ID: 129662940, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129662940
Gene description
ReSE screen-validated silencer GRCh37_chr11:61197385-61197720
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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 LOC129662940 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 (61429885..61430254)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61418784..61419152)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61197357..61197726)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61129243-61129964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4797 Neighboring gene transmembrane protein 138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61159824-61160785 Neighboring gene transmembrane protein 216 Neighboring gene cleavage and polyadenylation specific factor 7 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61196662-61197310 Neighboring gene succinate dehydrogenase complex assembly factor 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61213814-61214561 Neighboring gene RNA, 7SL, cytoplasmic 23, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr11:61225919-61226100 Neighboring gene Sharpr-MPRA regulatory region 8840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61253575-61254394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61255818-61256485 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61256486-61257152 Neighboring gene stabilizer of axonemal microtubules 4

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 active region 4798
  • ATAC-STARR-seq lymphoblastoid silent region 3393

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_159946.2 

    Range
    101..470
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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
    61429885..61430254
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    61418784..61419152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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