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LOC129390865 MPRA-validated peak2825 silencer [ Homo sapiens (human) ]

Gene ID: 129390865, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390865
Gene description
MPRA-validated peak2825 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 LOC129390865 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (36652840..36653040)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (37639180..37639380)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (35009295..35009495)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985031 Neighboring gene dehydrogenase/reductase 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:34983260-34983760 Neighboring gene mitochondrial rRNA methyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:34998295-34999169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35010359-35010858 Neighboring gene VISTA enhancer hs362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35013913-35014450 Neighboring gene uncharacterized LOC105371750 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:35018784-35018989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35021739-35022238 Neighboring gene uncharacterized LOC105371751 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:35109266-35109439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35148027-35148528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35169882-35170594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35170595-35171307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35173923-35174428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35174429-35174934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35183956-35184456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35184457-35184957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35194089-35194756 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:35207061-35208260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35215835-35216366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35219226-35220198 Neighboring gene Sharpr-MPRA regulatory region 13221 Neighboring gene LHX1 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 9746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35275423-35275942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35275943-35276460 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:35278241-35279440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35289047-35289564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35289565-35290082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35290165-35291080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:35292909-35293822

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_156495.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    36652840..36653040
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    888360..888560
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    37639180..37639380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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