U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129661207 ReSE screen-validated silencer GRCh37_chr4:981121-981298 [ Homo sapiens (human) ]

Gene ID: 129661207, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129661207
Gene description
ReSE screen-validated silencer GRCh37_chr4:981121-981298
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 K562 erythroleukemia cells. This locus also represents an accessible chromatin region 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC129661207 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 (986901..987550)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (985032..985681)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (980689..981338)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21140 Neighboring gene transmembrane protein 175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:938924-939517 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:957241-957400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:961731-962444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:962445-963158 Neighboring gene uncharacterized LOC124900645 Neighboring gene diacylglycerol kinase theta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:963506-964024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:965861-966501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:973450-974030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21141 Neighboring gene solute carrier family 26 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:983059-983560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:983561-984060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:986529-987340 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:987341-988152 Neighboring gene alpha-L-iduronidase Neighboring gene uncharacterized LOC124900646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:997000-997557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1003737-1004369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1007938-1008741 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1008742-1009544 Neighboring gene fibroblast growth factor receptor like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1011927-1012796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1019533-1020034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1020035-1020534

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 15116

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_158244.2 

    Range
    101..750
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    986901..987550
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    985032..985681
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases