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LOC108228205 PTPDC1-MIRLET7DHG intergenic CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108228205, updated on 17-Sep-2024

Summary

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Gene symbol
LOC108228205
Gene description
PTPDC1-MIRLET7DHG intergenic CAGE-defined high expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
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 element is located in the intergenic region between the PTPDC1 (protein tyrosine phosphatase domain containing 1) and MIRLET7DHG (MIRLET7D host gene) genes. It was defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). A subregion was validated as a functional enhancer by reporter assays in HeLa cells. This locus also includes an accessible chromatin subregion 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 LOC108228205 in Genome Data Viewer
Location:
9q22.32
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (94165623..94166682)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (106333681..106334740)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (96927905..96928964)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase domain containing 1 Neighboring gene CYCS pseudogene 24 Neighboring gene Sharpr-MPRA regulatory region 768 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96856496-96857248 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96880956-96881652 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110048 Neighboring gene tripartite motif-containing protein 54-like Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110072 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20053 Neighboring gene miRlet-7a-1/let-7f-1/let-7d cluster host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20054 Neighboring gene microRNA let-7a-1 Neighboring gene microRNA let-7f-1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 silent region 20052
  • PTPDC1-MIRLET7DHG interval high CAGE FANTOM5 enhancer

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_050977.2 

    Range
    101..1160
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    94165623..94166682
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    106333681..106334740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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