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LOC129935737 ATAC-STARR-seq lymphoblastoid silent region 12399 [ Homo sapiens (human) ]

Gene ID: 129935737, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935737
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12399
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 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]
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Genomic context

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See LOC129935737 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (227472145..227472864)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (227954832..227955551)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (228336861..228337580)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17202 Neighboring gene uncharacterized LOC124907994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:228335785-228336748 Neighboring gene microRNA 5703 Neighboring gene ArfGAP with FG repeats 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:228451619-228452120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12401 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57064 Neighboring gene small cysteine and glycine repeat containing 9 (pseudogene) Neighboring gene small cysteine and glycine repeat containing 2

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. 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)

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_168748.1 

    Range
    101..820
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    227472145..227472864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    227954832..227955551
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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