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SNHG21 small nucleolar RNA host gene 21 [ Homo sapiens (human) ]

Gene ID: 100505616, updated on 10-Oct-2023

Summary

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Official Symbol
SNHG21provided by HGNC
Official Full Name
small nucleolar RNA host gene 21provided by HGNC
Primary source
HGNC:HGNC:50284
See related
Ensembl:ENSG00000250988 AllianceGenome:HGNC:50284
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FSD2-AS1; SCARNA15HG
Expression
Ubiquitous expression in brain (RPKM 3.2), prostate (RPKM 3.0) and 25 other tissues See more
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Genomic context

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Location:
15q25.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (82750564..82757206)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (80614830..80621470)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (83419316..83425958)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene epididymal protein pseudogene Neighboring gene actin gamma 1 pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9965 Neighboring gene MPRA-validated peak2404 silencer Neighboring gene small Cajal body-specific RNA 15 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:83450989-83451154 Neighboring gene fibronectin type III and SPRY domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6756 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:83501038-83502237 Neighboring gene WASP homolog associated with actin, golgi membranes and microtubules Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:83518553-83519328 Neighboring gene homer scaffold protein 2 Neighboring gene uncharacterized LOC105370928

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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Related articles in PubMed

  1. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549
  2. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Antoniali G, et al. Nat Commun, 2017 Oct 6. PMID 28986522, Free PMC Article
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

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

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Other Names

  • FSD2 antisense RNA 1
  • RP11-752G15.6
  • small nucleolar RNA host gene 21 (non-protein coding)

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.

RNA

  1. NR_110096.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AA284521, BX112407, DB154257
    Related
    ENST00000561107.5

  2. NR_110097.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' region resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AA284521, CK904397, DB154257
    Related
    ENST00000559366.1

  3. NR_110098.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AA284521, CF129490, DB154257
    Related
    ENST00000558174.5

  4. NR_110099.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 3' region resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    DA396616, DA514642, DB154257
    Related
    ENST00000544685.2

  5. NR_110100.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses alternate splice sites in the 5' and 3' regions resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    DA514642, DB154257
    Related
    ENST00000558687.1

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
    82750564..82757206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    80614830..80621470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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