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LOC129391142 MPRA-validated peak3560 silencer [ Homo sapiens (human) ]

Gene ID: 129391142, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129391142
Gene description
MPRA-validated peak3560 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 LOC129391142 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 (54875539..54875739)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57969858..57970058)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55386995..55387195)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2 Neighboring gene RNA, U6 small nuclear 222, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15416 Neighboring gene Fc alpha receptor Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55404005-55404755 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55404756-55405506 Neighboring gene natural cytotoxicity triggering receptor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55431695-55432196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55432197-55432696 Neighboring gene NLR family pyrin domain containing 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55450505-55451214 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:55461990-55462680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55463371-55464060 Neighboring gene NLR family pyrin domain containing 2 Neighboring gene ribosomal protein L36a pseudogene 50

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_156772.1 

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

    Range
    54875539..54875739
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107304.1 Reference GRCh38.p14 PATCHES

    Range
    204612..204812
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Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107306.1 Reference GRCh38.p14 PATCHES

    Range
    176137..176337
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Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107308.1 Reference GRCh38.p14 PATCHES

    Range
    97924..98124
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107311.1 Reference GRCh38.p14 PATCHES

    Range
    96661..96861
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107312.1 Reference GRCh38.p14 PATCHES

    Range
    36247..36447 complement
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Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    520807..521007
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Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    779914..780114
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

    Range
    858109..858309
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_15

Genomic

  1. NT_187641.1 Reference GRCh38.p14 ALT_REF_LOCI_15

    Range
    5453..5653 complement
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Reference GRCh38.p14 ALT_REF_LOCI_23

Genomic

  1. NT_187671.1 Reference GRCh38.p14 ALT_REF_LOCI_23

    Range
    154486..154686
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Reference GRCh38.p14 ALT_REF_LOCI_26

Genomic

  1. NT_187674.1 Reference GRCh38.p14 ALT_REF_LOCI_26

    Range
    161559..161759
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Reference GRCh38.p14 ALT_REF_LOCI_27

Genomic

  1. NT_187675.1 Reference GRCh38.p14 ALT_REF_LOCI_27

    Range
    245778..245978
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Reference GRCh38.p14 ALT_REF_LOCI_28

Genomic

  1. NT_187676.1 Reference GRCh38.p14 ALT_REF_LOCI_28

    Range
    151489..151689
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Reference GRCh38.p14 ALT_REF_LOCI_29

Genomic

  1. NT_187677.1 Reference GRCh38.p14 ALT_REF_LOCI_29

    Range
    152906..153106
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Reference GRCh38.p14 ALT_REF_LOCI_30

Genomic

  1. NT_187683.1 Reference GRCh38.p14 ALT_REF_LOCI_30

    Range
    149757..149957
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    57969858..57970058
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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