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LOC129662600 ReSE screen-validated silencer GRCh37_chr9:140330497-140330751 [ Homo sapiens (human) ]

Gene ID: 129662600, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129662600
Gene description
ReSE screen-validated silencer GRCh37_chr9:140330497-140330751
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 HepG2 liver carcinoma cells. This locus also includes an accessible chromatin subregion 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]
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Genomic context

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See LOC129662600 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137436045..137436310)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149686667..149686932)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140330497..140330762)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene exonuclease 3'-5' domain containing 3 Neighboring gene uncharacterized LOC124902354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140323354-140324108 Neighboring gene Sharpr-MPRA regulatory region 12030 Neighboring gene NADPH oxidase activator 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140343721-140344920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140346657-140347540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140347541-140348422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20624 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140349307-140350188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140351970-140352667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20625 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140355491-140356424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140356425-140357357 Neighboring gene microRNA 7114 Neighboring gene NMDA receptor synaptonuclear signaling and neuronal migration factor Neighboring gene patatin like phospholipase domain containing 7 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140377541-140378740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140389307-140389807 Neighboring gene 9q34.3 PNPLA7 recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140438353-140438854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140443963-140444464

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 silent region 20622

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_159612.2 

    Range
    101..366
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137436045..137436310
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149686667..149686932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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