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LOC129391001 MPRA-validated peak3167 silencer [ Homo sapiens (human) ]

Gene ID: 129391001, updated on 12-Sep-2024

Summary

Gene symbol
LOC129391001
Gene description
MPRA-validated peak3167 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

See LOC129391001 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (57901824..57902024)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (58102026..58102226)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (55569056..55569256)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATPase phospholipid transporting 8B1 Neighboring gene uncharacterized LOC124904310 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:55443057-55444256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:55470167-55470804 Neighboring gene Sharpr-MPRA regulatory region 4888 Neighboring gene MPRA-validated peak3165 silencer Neighboring gene Sharpr-MPRA regulatory region 13131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13380 Neighboring gene ribosomal L24 domain containing 1 pseudogene 11 Neighboring gene NANOG hESC enhancer GRCh37_chr18:55523486-55524043 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:55561711-55562212 Neighboring gene uncharacterized LOC105372140 Neighboring gene long intergenic non-protein coding RNA 1897 Neighboring gene Sharpr-MPRA regulatory region 3246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13381 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 30

Genomic regions, transcripts, and products

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_156631.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    57901824..57902024
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    58102026..58102226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)