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VPS39-DT VPS39 divergent transcript [ Homo sapiens (human) ]

Gene ID: 105370795, updated on 10-Oct-2023

Summary

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Official Symbol
VPS39-DTprovided by HGNC
Official Full Name
VPS39 divergent transcriptprovided by HGNC
Primary source
HGNC:HGNC:55378
See related
AllianceGenome:HGNC:55378
Gene type
ncRNA
RefSeq status
MODEL
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Biased expression in testis (RPKM 2.0), bone marrow (RPKM 0.4) and 13 other tissues See more
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Genomic context

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Location:
15q15.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (42208401..42231192)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (40014399..40037224)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42438231-42438731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42441913-42442700 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:42442839-42442991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42446257-42446767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42448559-42449274 Neighboring gene phospholipase A2 group IVF Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42451565-42452064 Neighboring gene VPS39 subunit of HOPS complex Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9296 Neighboring gene microRNA 627 Neighboring gene transmembrane protein 87A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9298 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:42565593-42566792 Neighboring gene glucosidase alpha, neutral C Neighboring gene BCL2 interacting protein 3 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42652107-42652607 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:42655654-42656620 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42676684-42677239 Neighboring gene uncharacterized LOC105370794 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:42677734-42678933 Neighboring gene calpain 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

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 studies and variants in dbVar

Genotypes

NCBI Reference Sequences (RefSeq)

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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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    42208401..42231192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_932181.3 RNA Sequence

  2. XR_932179.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    40014399..40037224
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_007085916.1 RNA Sequence

  2. XR_007085914.1 RNA Sequence

  3. XR_007085913.1 RNA Sequence

  4. XR_007085915.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version

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