Aliases for SCARNA13 Gene

Data sources for SCARNA13 Gene:

Subcategory (RNA class) for SCARNA13 Gene

snoRNA

Aliases for SCARNA13 Gene

External Ids for SCARNA13 Gene

Previous GeneCards Identifiers for SCARNA13 Gene

  • GC14U900662
  • GC14M095071
  • GC14M095999
  • GC14M076185

Summaries for SCARNA13 Gene

GeneCards Summary for SCARNA13 Gene

SCARNA13 (Small Cajal Body-Specific RNA 13) is an RNA Gene, and is affiliated with the snoRNA class. Diseases associated with SCARNA13 include Koolen-De Vries Syndrome.

Rfam classification for SCARNA13 Gene

  • Small Cajal body specific RNA 13

Additional gene information for SCARNA13 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 SCARNA13 Gene

Genomics for SCARNA13 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCARNA13 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
GH14J095530 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 267.7 -1.2 -1246 8.8 ZSCAN16 TBP SP1 CEBPA NR2C1 FOXA1 MNT IKZF1 SMAD5 ETS1 GLRX5 SNHG10 SCARNA13 SYNE3 PAPOLA DICER1 ENSG00000258572 TCL1B
GH14J095259 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 74.3 +270.5 270475 9.5 BCL11A MXD4 SP1 CEBPA DEK ZNF217 ELF1 ZIC2 HOMEZ THAP11 SNHG10 SCARNA13 DICER1 CLMN piR-36588-165 piR-38352-184
GH14J095155 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 31.8 +376.7 376728 3.8 ZSCAN16 CHD2 ZBTB10 SP1 FEZF1 NR2C1 MNT SMAD5 MBD2 ZNF217 DICER1 DICER1-AS1 lnc-DICER1-2 SCARNA13 SNHG10 MIR3173 GSC
GH14J096390 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 27.4 -858.4 -858372 2.8 SP1 MNT SMAD5 POLR2A BHLHE40 ZEB1 ZIC2 SIN3A ZNF639 MAX AK7 lnc-ATG2B-11 PAPOLA SCARNA13 SNHG10 GSKIP
GH14J094768 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 19.9 +764.1 764128 2.2 ZNF341 CTBP1 SIN3A KLF9 YY1 SP2 KLF16 CBX8 SMARCE1 POLR2A ENSG00000285205 GSC GSC-DT HSALNG0103390 SCARNA13 SNHG10 DICER1 RPSAP4 SERPINA3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCARNA13 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the SCARNA13 gene promoter:
  • E47
  • GR
  • GR-alpha
  • GR-beta
  • NF-kappaB1
  • Nkx2-5
  • Nkx5-1
  • Pax-5
  • POU2F1
  • POU2F1a

Genomic Locations for SCARNA13 Gene

Latest Assembly
chr14:95,533,354-95,533,629
(GRCh38/hg38)
Size:
276 bases
Orientation:
Minus strand

Previous Assembly
chr14:95,999,692-95,999,966
(GRCh37/hg19 by Entrez Gene)
Size:
275 bases
Orientation:
Minus strand

chr14:95,999,692-95,999,966
(GRCh37/hg19 by Ensembl)
Size:
275 bases
Orientation:
Minus strand

Genomic View for SCARNA13 Gene

Genes around SCARNA13 on UCSC Golden Path with GeneCards custom track
SCARNA13 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
SCARNA13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA13 Gene

Proteins for SCARNA13 Gene

Post-translational modifications for SCARNA13 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA13 Gene

Domains & Families for SCARNA13 Gene

Gene Families for SCARNA13 Gene

genes like me logo Genes that share domains with SCARNA13: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SCARNA13 Gene

Function for SCARNA13 Gene

Phenotypes From GWAS Catalog for SCARNA13 Gene

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SCARNA13 Gene

Localization for SCARNA13 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 SCARNA13 gene
Compartment Confidence
nucleus 1

Gene Ontology (GO) - Cellular Components for SCARNA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IEA --
GO:0015030 Cajal body IMP 25467444
genes like me logo Genes that share ontologies with SCARNA13: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for SCARNA13 Gene

Pathways & Interactions for SCARNA13 Gene

PathCards logo

SuperPathways for SCARNA13 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCARNA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SCARNA13: view

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for SCARNA13 Gene

Drugs & Compounds for SCARNA13 Gene

No Compound Related Data Available

Transcripts for SCARNA13 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for SCARNA13 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000026BDF0_9606 snoRNA 275 8

RefSeq: NR_003002,

Ensembl: ENST00000516672 (view in UCSC) ,

LncBook: HSALNT0215211, HSALNT0215212,

LNCipedia: SNHG10:11,

Rfam: RF00231,

snoDB: SNODB82,

snOPY: Homo_sapiens300781,

ENA: AF492209.1:1..275:ncRNA,

URS00008B8360_9606 lncRNA 1330 3

LncBook: HSALNT0215205,

LNCipedia: SNHG10:4,

NONCODE: NONHSAT039454.2,

URS00008C03DF_9606 lncRNA 1074 3

LncBook: HSALNT0215202,

LNCipedia: SNHG10:9,

NONCODE: NONHSAT039453.2,

URS00008BBB69_9606 lncRNA 3200 2

LNCipedia: SNHG10:1,

NONCODE: NONHSAT039451.2,

URS00008B2331_9606 lncRNA 1961 2

LNCipedia: SNHG10:5,

NONCODE: NONHSAT039455.2,

SCARNA13 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for SCARNA13 Gene

1 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA13 Gene

No ASD Table

Relevant External Links for SCARNA13 Gene

GeneLoc Exon Structure for
SCARNA13

Expression for SCARNA13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCARNA13 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCARNA13

genes like me logo Genes that share expression patterns with SCARNA13: 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 SCARNA13 Gene

Orthologs for SCARNA13 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCARNA13 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SCARNA13 31
  • 99 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Scarna13 31
  • 86 (a)
OneToMany
Gm25624 31
  • 79 (a)
OneToMany
Gm26489 31
  • 78 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia SCARNA13 31
  • 83 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SCARNA13 31
  • 80 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SCARNA13 31
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SCARNA13 31
  • 72 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SCARNA13 31
  • 74 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SCARNA13 31
  • 68 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii SCARNA13 31
  • 56 (a)
OneToOne
Species where no ortholog for SCARNA13 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • 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 SCARNA13 Gene

ENSEMBL:
Gene Tree for SCARNA13 (if available)
TreeFam:
Gene Tree for SCARNA13 (if available)

Paralogs for SCARNA13 Gene

No data available for Paralogs for SCARNA13 Gene

Variants for SCARNA13 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SCARNA13 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 SCARNA13 Gene

Variant ID Type Subtype PubMed ID
dgv89e55 CNV gain 17911159
esv3635400 CNV gain 21293372
nsv1042858 CNV gain 25217958
nsv565631 CNV gain 21841781

Additional Variant Information for SCARNA13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA13

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 SCARNA13 Gene

Disorders for SCARNA13 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCARNA13 Gene - From: COP

Disorder Aliases PubMed IDs
koolen-de vries syndrome
  • kdvs
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCARNA13

genes like me logo Genes that share disorders with SCARNA13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCARNA13 Gene

Publications for SCARNA13 Gene

  1. A Cajal body-specific pseudouridylation guide RNA is composed of two box H/ACA snoRNA-like domains. (PMID: 12409454) Kiss AM … Kiss T (Nucleic acids research 2002) 2 3
  2. SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing. (PMID: 26867678) Chen S … Voit R (Nature communications 2016) 3
  3. Proteostatic control of telomerase function through TRiC-mediated folding of TCAB1. (PMID: 25467444) Freund A … Artandi SE (Cell 2014) 3
  4. hNaf1 is required for accumulation of human box H/ACA snoRNPs, scaRNPs, and telomerase. (PMID: 16601202) Hoareau-Aveilla C … Henry Y (RNA (New York, N.Y.) 2006) 3

Products for SCARNA13 Gene

Sources for SCARNA13 Gene