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LOC129390945 MPRA-validated peak3024 silencer [ Homo sapiens (human) ]

Gene ID: 129390945, updated on 12-Sep-2024

Summary

Gene symbol
LOC129390945
Gene description
MPRA-validated peak3024 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

See LOC129390945 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 (80376556..80376756)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (81278415..81278615)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78350356..78350556)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene caspase recruitment domain family member 14 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:78178385-78179584 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:78183891-78184046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78195951-78196788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78196789-78197626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78200105-78200606 Neighboring gene N-sulfoglucosamine sulfohydrolase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78209849-78210638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78210639-78211426 Neighboring gene solute carrier family 26 member 11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78227308-78228024 Neighboring gene SLC26A11-RNF213 intergenic CAGE-defined mid-level expression enhancer Neighboring gene CRISPRi-validated cis-regulatory element chr17.5742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78237270-78237826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78247837-78248435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78251821-78252439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78258533-78259093 Neighboring gene ring finger protein 213 Neighboring gene RNF213 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:78345568-78346767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78354122-78354622 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:78359110-78360309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78369069-78369570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371216-78371723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371724-78372230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78398753-78399254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78399255-78399754 Neighboring gene microRNA 4730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78415272-78415938 Neighboring gene endonuclease V Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78419431-78420213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78428217-78429046 Neighboring gene Sharpr-MPRA regulatory region 4093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78441725-78442449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78448861-78449394 Neighboring gene neuronal pentraxin 1

Genomic regions, transcripts, and products

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_156575.1 

    Range
    101..301
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    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
    80376556..80376756
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    81278415..81278615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)