Aliases for SCARNA23 Gene

Data sources for SCARNA23 Gene:

RNA type for SCARNA23 Gene

snoRNA

Aliases for SCARNA23 Gene

External Ids for SCARNA23 Gene

Previous GeneCards Identifiers for SCARNA23 Gene

  • GC0XP024672
  • GC0XP024762
  • GC0XP022505

Summaries for SCARNA23 Gene

GeneCards Summary for SCARNA23 Gene

SCARNA23 (Small Cajal Body-Specific RNA 23) is an RNA Gene, and is affiliated with the snoRNA class. Diseases associated with SCARNA23 include Warburg Micro Syndrome 1 and Dyskeratosis Congenita, X-Linked.

Rfam classification for SCARNA23 Gene

  • Small Cajal body specific RNA 24

Additional gene information for SCARNA23 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for SCARNA23 Gene

Genomics for SCARNA23 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCARNA23 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ024720 Enhancer 0.3 Ensembl 13.2 -24.2 -24240 0.4 PRDM1 SCARNA23 POLA1 lnc-PCYT1B-1 piR-43105-696 RF00017-7644 ARX
GH0XJ024733 Enhancer 0.6 FANTOM5 Ensembl ENCODE 0.4 -11.2 -11240 1.2 SPI1 PCYT1B RANBP1P1 piR-43105-696 SCARNA23 POLA1 RF00017-7644 ARX
GH0XJ024741 Enhancer 0.3 VISTA 0.7 -2.9 -2936 0.5 NFIC ZSCAN4 SCARNA23 piR-43105-696 POLA1 RF00017-7644 ARX
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCARNA23 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the SCARNA23 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • FOXD3
  • POU2F1
  • SRF
  • SRF (504 AA)

Genomic Locations for SCARNA23 Gene

Latest Assembly
chrX:24,744,441-24,744,570
(GRCh38/hg38)
Size:
130 bases
Orientation:
Plus strand

Previous Assembly
chrX:24,762,558-24,762,687
(GRCh37/hg19 by Entrez Gene)
Size:
130 bases
Orientation:
Plus strand

chrX:24,762,558-24,762,687
(GRCh37/hg19 by Ensembl)
Size:
130 bases
Orientation:
Plus strand

Genomic View for SCARNA23 Gene

Genes around SCARNA23 on UCSC Golden Path with GeneCards custom track
SCARNA23 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
SCARNA23 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA23 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA23 Gene

Proteins for SCARNA23 Gene

Post-translational modifications for SCARNA23 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA23 Gene

Domains & Families for SCARNA23 Gene

Gene Families for SCARNA23 Gene

genes like me logo Genes that share domains with SCARNA23: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SCARNA23 Gene

Function for SCARNA23 Gene

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SCARNA23 Gene

Localization for SCARNA23 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCARNA23 gene
Compartment Confidence
nucleus 1

Gene Ontology (GO) - Cellular Components for SCARNA23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IEA --
GO:0015030 Cajal body IEA --
genes like me logo Genes that share ontologies with SCARNA23: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for SCARNA23 Gene

Pathways & Interactions for SCARNA23 Gene

PathCards logo

SuperPathways for SCARNA23 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCARNA23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SCARNA23: view

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for SCARNA23 Gene

Drugs & Compounds for SCARNA23 Gene

No Compound Related Data Available

Transcripts for SCARNA23 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for SCARNA23 Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS0000466492_9606 snoRNA 130 6

RefSeq: NR_003007,

Ensembl: ENST00000516060 (view in UCSC) ,

Rfam: RF00422,

snoDB: SNODB178,

snOPY: Homo_sapiens300788,

ENA: AJ609482.1:1..130:ncRNA,

URS0001BC1F71_9606 snoRNA 130 1

Rfam: RF00422,

SCARNA23 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for SCARNA23 Gene

1 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA23 Gene

No ASD Table

Relevant External Links for SCARNA23 Gene

GeneLoc Exon Structure for
SCARNA23

Expression for SCARNA23 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCARNA23 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCARNA23

SOURCE GeneReport for Unigene cluster for SCARNA23 Gene:

Hs.689695
genes like me logo Genes that share expression patterns with SCARNA23: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCARNA23 Gene

Orthologs for SCARNA23 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCARNA23 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SCARNA24 30
  • 99 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SCARNA24 30
  • 93 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SCARNA24 30
  • 90 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SCARNA24 30
  • 74 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Gm23557 30
  • 71 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SCARNA24 30
  • 69 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii SCARNA24 30
  • 52 (a)
OneToMany
Species where no ortholog for SCARNA23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SCARNA23 Gene

ENSEMBL:
Gene Tree for SCARNA23 (if available)
TreeFam:
Gene Tree for SCARNA23 (if available)
Alliance of Genome Resources:
Additional Orthologs for SCARNA23

Paralogs for SCARNA23 Gene

No data available for Paralogs for SCARNA23 Gene

Variants for SCARNA23 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SCARNA23 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SCARNA23 Gene

Variant ID Type Subtype PubMed ID
nsv517960 CNV gain 19592680

Additional Variant Information for SCARNA23 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA23
Leiden Open Variation Database (LOVD)
SCARNA23

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for SCARNA23 Gene

Disorders for SCARNA23 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SCARNA23 Gene - From: COP

Disorder Aliases PubMed IDs
warburg micro syndrome 1
  • warbm1
dyskeratosis congenita, x-linked
  • dkcx
urethral stricture
dyskeratosis congenita
  • zinsser-cole-engman syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCARNA23

genes like me logo Genes that share disorders with SCARNA23: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCARNA23 Gene

Publications for SCARNA23 Gene

  1. SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing. (PMID: 26867678) Chen S … Voit R (Nature communications 2016) 3
  2. Box H/ACA small ribonucleoproteins. (PMID: 20227365) Kiss T … Jády BE (Molecular cell 2010) 3
  3. Human box H/ACA pseudouridylation guide RNA machinery. (PMID: 15199136) Kiss AM … Kiss T (Molecular and cellular biology 2004) 3
  4. Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs. (PMID: 12032087) Darzacq X … Kiss T (The EMBO journal 2002) 3

Products for SCARNA23 Gene

Sources for SCARNA23 Gene