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LOC129391093 MPRA-validated peak3442 silencer [ Homo sapiens (human) ]

Gene ID: 129391093, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129391093
Gene description
MPRA-validated peak3442 silencer
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 region was identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. It was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
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Genomic context

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See LOC129391093 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (34259175..34259375)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (36786507..36786707)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (34750080..34750280)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34617551-34618060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10501 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:34625657-34626192 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 2 pseudogene 3 Neighboring gene LSM14A mRNA processing body assembly factor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:34715679-34716244 Neighboring gene MPRA-validated peak3441 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:34728773-34729345 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:34745756-34746277 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:34761021-34761721 Neighboring gene granule associated Rac and RHOG effector 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34801395-34801894 Neighboring gene ribosomal protein L29 pseudogene 33 Neighboring gene Sharpr-MPRA regulatory region 14193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34833051-34833551 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:34850825-34851431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34857175-34857915 Neighboring gene glucose-6-phosphate isomerase

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, 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_156723.1 

    Range
    101..301
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    34259175..34259375
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315963.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    114089..114289
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    36786507..36786707
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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