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LOC129661745 ReSE screen-validated silencer GRCh37_chr6:41461668-41461828 [ Homo sapiens (human) ]

Gene ID: 129661745, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129661745
Gene description
ReSE screen-validated silencer GRCh37_chr6:41461668-41461828
Gene type
biological region
Feature type(s)
regulatory: silencer, transcriptional_cis_regulatory_region
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 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, and was also shown to negatively regulate the FOXP4 (forkhead box P4) gene based on CRISPR/Cas9-mediated knockout in K562 cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129661745 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41493897..41494113)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41322934..41323150)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41461635..41461851)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100505711 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41374298-41375106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41375914-41376721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41376722-41377528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41396875-41397374 Neighboring gene uncharacterized LOC107986538 Neighboring gene VISTA enhancer hs2104 Neighboring gene uncharacterized LOC112267957 Neighboring gene Sharpr-MPRA regulatory region 8968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41424325-41425112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41438012-41438663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41459644-41460288 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41470387-41471134 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41471135-41471882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41473163-41473662 Neighboring gene long intergenic non-protein coding RNA 1276 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr6:41499390-41499960 and GRCh37_chr6:41499961-41500529 Neighboring gene FOXP4 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24511 Neighboring gene Sharpr-MPRA regulatory region 4049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17186 Neighboring gene forkhead box P4

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)

General gene information

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Other Names

  • FOXP4 negatively-actiing cis-regulatory element

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_158781.2 

    Range
    101..317
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    41493897..41494113
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    41322934..41323150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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