U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129390246 MPRA-validated peak1145 silencer [ Homo sapiens (human) ]

Gene ID: 129390246, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129390246
Gene description
MPRA-validated peak1145 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 LOC129390246 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (492756..492956)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (538478..538678)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (492756..492956)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376506 Neighboring gene anoctamin 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3005 Neighboring gene Sharpr-MPRA regulatory region 223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:442612-443409 Neighboring gene RNA, 7SL, cytoplasmic 838, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3007 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:449779-450465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:454927-455648 Neighboring gene phosphatidylserine synthase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:460662-460845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:467161-467660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:471334-471857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:471858-472380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:476893-477888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:484337-484858 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:487868-488008 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21531 Neighboring gene ribonuclease/angiogenin inhibitor 1 Neighboring gene leucine rich repeat containing 56 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:528505-529042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:533792-534649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:534650-535506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:535528-536235 Neighboring gene HRas proto-oncogene, GTPase

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_155876.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    492756..492956
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187586.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    22397..22597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    538478..538678
    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