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LOC129997877 ATAC-STARR-seq lymphoblastoid silent region 17912 [ Homo sapiens (human) ]

Gene ID: 129997877, updated on 12-Sep-2024

Summary

Gene symbol
LOC129997877
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17912
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 sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

See LOC129997877 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 (5282868..5283017)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (5400628..5400777)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (5322499..5322648)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak6354 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17909 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17910 Neighboring gene RNA, U6 small nuclear 215, pseudogene Neighboring gene WD repeat domain, phosphoinositide interacting 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:5257932-5259131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5262434-5263183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17911 Neighboring gene Sharpr-MPRA regulatory region 13937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5323448-5324013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5324014-5324580 Neighboring gene Sharpr-MPRA regulatory region 9837 Neighboring gene Sharpr-MPRA regulatory region 3727 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17913 Neighboring gene solute carrier family 29 member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5350589-5351090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5351091-5351590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5362189-5362722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5362723-5363256 Neighboring gene trinucleotide repeat containing 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5387551-5388392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5390077-5390917 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5395754-5396256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5421456-5422020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5422021-5422584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5441055-5441556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5443987-5444488 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5447331-5447920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5447921-5448510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5458249-5458998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5467243-5467992 Neighboring gene long intergenic non-protein coding RNA 2983 Neighboring gene long intergenic non-protein coding RNA 3073

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_177318.1 

    Range
    101..250
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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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    5282868..5283017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    5400628..5400777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)