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LOC129388442 MPRA-validated peak57 silencer [ Homo sapiens (human) ]

Gene ID: 129388442, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388442
Gene description
MPRA-validated peak57 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 LOC129388442 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (9711297..9711497)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (9254077..9254277)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (9771355..9771555)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta Neighboring gene ribosomal protein L26 pseudogene 7 Neighboring gene PIK3CD antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 229 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9748072-9748266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9749677-9750360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9750361-9751042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9761057-9761631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9769519-9770216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9775415-9776390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9776391-9777366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 231 Neighboring gene uncharacterized LOC124903839 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:9778914-9780113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9780296-9781272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9781273-9782247 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9785121-9785329 Neighboring gene calsyntenin 1 Neighboring gene MPRA-validated peak58 silencer Neighboring gene mitotic spindle organizing protein 1 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 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_154076.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    9711297..9711497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    9254077..9254277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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