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LOC129935874 ATAC-STARR-seq lymphoblastoid silent region 12466 [ Homo sapiens (human) ]

Gene ID: 129935874, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935874
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12466
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 LOC129935874 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 (233060497..233060576)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (233547847..233547926)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (233925207..233925286)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neuronal guanine nucleotide exchange factor Neighboring gene uncharacterized LOC101928881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233927377-233927970 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233926783-233927376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233937995-233938700 Neighboring gene neuraminidase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17332 Neighboring gene Sharpr-MPRA regulatory region 10619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233953501-233954000 Neighboring gene inositol polyphosphate-5-phosphatase D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972623-233973122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972121-233972622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233982267-233982860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:233987251-233987751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233988888-233989435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233989436-233989982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233993677-233994176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234072305-234072918 Neighboring gene NANOG hESC enhancer GRCh37_chr2:234125377-234125936 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234131944-234132095 Neighboring gene RNA, 7SL, cytoplasmic 32, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234151441-234151635 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:234155927-234157126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12469 Neighboring gene autophagy related 16 like 1 Neighboring gene small Cajal body-specific RNA 5

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 variants in ClinVar

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_168885.1 

    Range
    101..180
    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
    233060497..233060576
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332690.1 Reference GRCh38.p14 PATCHES

    Range
    5835..5914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    233547847..233547926
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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