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LOC124416875 Sharpr-MPRA regulatory region 13404 [ Homo sapiens (human) ]

Gene ID: 124416875, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416875
Gene description
Sharpr-MPRA regulatory region 13404
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC124416875 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (95865244..95865586)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (96744343..96744685)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (97625049..97625343)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3716 Neighboring gene aldehyde dehydrogenase 18 family member A1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3801 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97454143-97454644 Neighboring gene tectonic family member 3 Neighboring gene MPRA-validated peak1056 silencer Neighboring gene ectonucleoside triphosphate diphosphohydrolase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2650 Neighboring gene ENTPD1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3811 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:97645298-97645457 Neighboring gene MPRA-validated peak1059 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3814 Neighboring gene coiled-coil and C2 domain containing 2B Neighboring gene ribosomal protein L21 pseudogene 90 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:97786197-97787396 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:97802729-97802923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2652 Neighboring gene cyclin J

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 3812

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_079097.2 

    Range
    101..443
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    95865244..95865586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    96744343..96744685
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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