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LOC129389704 MPRA-validated peak6269 silencer [ Homo sapiens (human) ]

Gene ID: 129389704, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389704
Gene description
MPRA-validated peak6269 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 LOC129389704 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (158120103..158120303)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159366334..159366534)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (158541135..158541335)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene sorting nexin 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17730 Neighboring gene RNA, U6 small nuclear 786, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr6.5510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158394739-158395292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402145-158402660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402661-158403176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158420467-158420966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447101-158447788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447789-158448476 Neighboring gene SYNJ2 intronic transcript 1 Neighboring gene Sharpr-MPRA regulatory region 12557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158458586-158459280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158461967-158462502 Neighboring gene synaptojanin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158470498-158471112 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158490014-158491213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492197-158492760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492761-158493322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158516915-158517415 Neighboring gene serine active site containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604741-158605243 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604236-158604740 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:158615403-158616003 Neighboring gene general transcription factor IIH subunit 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:158653118-158653990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25349 Neighboring gene signal recognition particle 72 pseudogene 2 Neighboring gene TUB like protein 4

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_155334.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    158120103..158120303
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    159366334..159366534
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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