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LOC129389956 MPRA-validated peak6905 silencer [ Homo sapiens (human) ]

Gene ID: 129389956, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389956
Gene description
MPRA-validated peak6905 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 LOC129389956 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (11605807..11606007)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (8134230..8134430, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11463316..11463516)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene BLK proto-oncogene, Src family tyrosine kinase Neighboring gene uncharacterized LOC105379241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18935 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:11424419-11425618 Neighboring gene long intergenic non-protein coding RNA 208 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11456947-11457783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11478375-11478875 Neighboring gene Sharpr-MPRA regulatory region 10445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11487938-11488828 Neighboring gene uncharacterized LOC105379242 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:11530424-11530618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11532437-11532959 Neighboring gene VISTA enhancer hs2204 Neighboring gene GATA binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18936 Neighboring gene small nucleolar RNA, H/ACA box 99

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_155586.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    11605807..11606007
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    1742071..1742271 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    8134230..8134430 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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