U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129390820 MPRA-validated peak2677 silencer [ Homo sapiens (human) ]

Gene ID: 129390820, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129390820
Gene description
MPRA-validated peak2677 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC129390820 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 (1970981..1971181)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1859771..1859971)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1874275..1874475)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4981 Neighboring gene Sharpr-MPRA regulatory region 13179 Neighboring gene SET and MYND domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1734195-1734695 Neighboring gene replication protein A1 Neighboring gene SDHC pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810454-1810962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810963-1811470 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1825407-1825589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1834946-1835511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1835512-1836076 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1846458-1846649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1849416-1849974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851145-1851648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851649-1852150 Neighboring gene reticulon 4 receptor like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1866080-1866746 Neighboring gene NANOG hESC enhancer GRCh37_chr17:1879245-1879860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1885529-1886370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1886371-1887212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1889733-1890236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1890237-1890738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1894981-1895842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1895843-1896703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1903279-1903789 Neighboring gene uncharacterized LOC105371486 Neighboring gene uncharacterized LOC105371485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1927475-1928020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1929189-1929689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1933195-1933786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1933787-1934378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7968 Neighboring gene diphthamide biosynthesis 1 Neighboring gene OVCA2 serine hydrolase domain containing

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_156450.1 

    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
    1970981..1971181
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1859771..1859971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases