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LOC129389534 MPRA-validated peak5838 silencer [ Homo sapiens (human) ]

Gene ID: 129389534, updated on 12-Sep-2024

Summary

Gene symbol
LOC129389534
Gene description
MPRA-validated peak5838 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 LOC129389534 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (49693642..49693842)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (49535616..49535816)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (49661355..49661555)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 6456 Neighboring gene cytochrome P450 family 2 subfamily AC member 1, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:49553494-49553995 Neighboring gene MPRA-validated peak5837 silencer Neighboring gene Rh associated glycoprotein Neighboring gene GATA motif-containing MPRA enhancer 217 Neighboring gene Sharpr-MPRA regulatory region 4614 Neighboring gene cysteine rich secretory protein 2 Neighboring gene MPRA-validated peak5839 silencer Neighboring gene cysteine rich secretory protein 3 Neighboring gene phosphoglycerate kinase 2

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_155164.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    49693642..49693842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    49535616..49535816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)