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LOC129388903 MPRA-validated peak3833 silencer [ Homo sapiens (human) ]

Gene ID: 129388903, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388903
Gene description
MPRA-validated peak3833 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 LOC129388903 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (119649439..119649639)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (120082954..120083154)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (120407015..120407215)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:120189865-120190371 Neighboring gene transmembrane protein 37 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:120231245-120231796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:120232347-120232897 Neighboring gene secretin receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:120238515-120239026 Neighboring gene VISTA enhancer hs1941 Neighboring gene SCTR antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11906 Neighboring gene cilia and flagella associated protein 221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11909 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11911 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:120457784-120458983 Neighboring gene transmembrane protein 177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:120459450-120460055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:120460663-120461267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:120472887-120473388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:120473389-120473888 Neighboring gene ribosomal protein L17 pseudogene 15 Neighboring gene uncharacterized LOC101927764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11912 Neighboring gene Sharpr-MPRA regulatory region 5959

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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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_154536.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    119649439..119649639
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    120082954..120083154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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