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LOC130005067 ATAC-STARR-seq lymphoblastoid silent region 3003 [ Homo sapiens (human) ]

Gene ID: 130005067, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005067
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3003
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

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See LOC130005067 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (416892..416971)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (462345..462424)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (416892..416971)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene beta-1,4-N-acetyl-galactosaminyltransferase 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:380111-380268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:393662-394424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:396383-396912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:405522-406215 Neighboring gene plakophilin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:415472-416091 Neighboring gene single Ig and TIR domain containing Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:420870-421731 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:428546-429745 Neighboring gene anoctamin 9 Neighboring gene uncharacterized LOC105376506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:434102-434620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3005 Neighboring gene Sharpr-MPRA regulatory region 223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:442612-443409 Neighboring gene RNA, 7SL, cytoplasmic 838, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3007 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:449779-450465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:454927-455648 Neighboring gene phosphatidylserine synthase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:460662-460845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:467161-467660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:471334-471857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:471858-472380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:476893-477888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:484337-484858 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:487868-488008

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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_184512.1 

    Range
    101..180
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    416892..416971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    462345..462424
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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