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LOC129389965 MPRA-validated peak6942 silencer [ Homo sapiens (human) ]

Gene ID: 129389965, updated on 12-Sep-2024

Summary

Gene symbol
LOC129389965
Gene description
MPRA-validated peak6942 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 LOC129389965 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 (23120162..23120362)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (23395104..23395304)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (22977675..22977875)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene TNF receptor superfamily member 10b Neighboring gene TNFRSF10B antisense RNA 1 Neighboring gene TNFRSF10B 5' regulatory region Neighboring gene Sharpr-MPRA regulatory region 12406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22928365-22928864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22941919-22942800 Neighboring gene uncharacterized LOC254896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22960499-22961308 Neighboring gene TNF receptor superfamily member 10c Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22976378-22976878 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19020 Neighboring gene TNF receptor superfamily member 10d Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23002103-23002830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27108 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:23025986-23026166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23031113-23031614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23033956-23034512 Neighboring gene TNF receptor superfamily member 10a Neighboring gene ribosomal protein L23a pseudogene 55

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_155595.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    23120162..23120362
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    23395104..23395304
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    GenBank, FASTA, Sequence Viewer (Graphics)