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SCARNA13 small Cajal body-specific RNA 13 [ Homo sapiens (human) ]

Gene ID: 677768, updated on 10-Oct-2023

Summary

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Official Symbol
SCARNA13provided by HGNC
Official Full Name
small Cajal body-specific RNA 13provided by HGNC
Primary source
HGNC:HGNC:32570
See related
Ensembl:ENSG00000252481 AllianceGenome:HGNC:32570
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
U93
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Genomic context

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Location:
14q32.13
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (95533355..95533629, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (89764048..89764322, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (95999692..95999966, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370640 Neighboring gene spectrin repeat containing nuclear envelope family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8958 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:95904894-95906093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95917656-95918448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95941052-95941938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95941939-95942824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95961573-95962074 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr14:95966308-95966888 and GRCh37_chr14:95966889-95967468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8962 Neighboring gene Sharpr-MPRA regulatory region 11978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8963 Neighboring gene SYNE3 antisense RNA 1 Neighboring gene CRISPRi-validated cis-regulatory element chr14.2067 Neighboring gene Sharpr-MPRA regulatory region 6741 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:95999817-96000606 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:96000607-96001396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6049 Neighboring gene CRISPRi-validated cis-regulatory element chr14.2077 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:96014120-96014995 Neighboring gene small nucleolar RNA host gene 10 Neighboring gene glutaredoxin 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:96024009-96024508 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:96042156-96043078 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:96043079-96044000 Neighboring gene long intergenic non-protein coding RNA 2318

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. A Cajal body-specific pseudouridylation guide RNA is composed of two box H/ACA snoRNA-like domains. Kiss AM, et al. Nucleic Acids Res, 2002 Nov 1. PMID 12409454, Free PMC Article
  2. Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13. Nagpal N, et al. Nucleic Acids Res, 2022 Sep 9. PMID 36018809, Free PMC Article
  3. hNaf1 is required for accumulation of human box H/ACA snoRNPs, scaRNPs, and telomerase. Hoareau-Aveilla C, et al. RNA, 2006 May. PMID 16601202, Free PMC Article
  4. Proteostatic control of telomerase function through TRiC-mediated folding of TCAB1. Freund A, et al. Cell, 2014 Dec 4. PMID 25467444, Free PMC Article
  5. SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing. Chen S, et al. Nat Commun, 2016 Feb 12. PMID 26867678, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13.
    Title: Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13.
Submit: New GeneRIF Correction

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

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in RNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Cajal body IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  

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_003002.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AF492209
    Related
    ENST00000516672.1

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    95533355..95533629 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    89764048..89764322 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases