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LOC129661306 ReSE screen-validated silencer GRCh37_chr4:89059146-89059357 [ Homo sapiens (human) ]

Gene ID: 129661306, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129661306
Gene description
ReSE screen-validated silencer GRCh37_chr4:89059146-89059357
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 ABCG2 (ATP binding cassette subfamily G member 2) gene based on CRISPR/Cas9-mediated knockouts in K562 cells and 293T embryonic kidney cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129661306 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (88137901..88138300)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (91464098..91464497)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (89059053..89059452)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15560 Neighboring gene RNA, U1 small nuclear 36, pseudogene Neighboring gene polycystin 2, transient receptor potential cation channel Neighboring gene Sharpr-MPRA regulatory region 5607 Neighboring gene ATP binding cassette subfamily G member 2 (JR blood group) Neighboring gene uncharacterized LOC124900867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15561 Neighboring gene Sharpr-MPRA regulatory region 2987 Neighboring gene ribosomal protein L31 pseudogene 24

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

  • ABCG2 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_158343.2 

    Range
    101..500
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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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    88137901..88138300
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    91464098..91464497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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