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LOC129389729 MPRA-validated peak6340 silencer [ Homo sapiens (human) ]

Gene ID: 129389729, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389729
Gene description
MPRA-validated peak6340 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 LOC129389729 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (1351179..1351379)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (1462164..1462365)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (1390815..1391015)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr7:1199449-1199961 and GRCh37_chr7:1199962-1200475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1200476-1200988 Neighboring gene ZFAND2A divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1209085-1210060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1210061-1211034 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17848 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:1220431-1221630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1232959-1233460 Neighboring gene Sharpr-MPRA regulatory region 5475 Neighboring gene VISTA enhancer hs293 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1273513-1274057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1274230-1275058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1281290-1282188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1288405-1288950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1294047-1294547 Neighboring gene MPRA-validated peak6338 silencer Neighboring gene UNC homeobox Neighboring gene MS31A repeat instability region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1329612-1330486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1341047-1341548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1360639-1361139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1409793-1410317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17851 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1458534-1459206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1459207-1459877 Neighboring gene Sharpr-MPRA regulatory region 11952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1468179-1468734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1486489-1486993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1491449-1492000 Neighboring gene Sharpr-MPRA regulatory region 3173 Neighboring gene MICAL like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1497060-1497782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1497783-1498505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1499929-1500480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1500481-1501032 Neighboring gene MICALL2 divergent transcript

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_155359.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    1351179..1351379
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    1462164..1462365
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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