Aliases for SCARNA16 Gene

Data sources for SCARNA16 Gene:

Subcategory (RNA class) for SCARNA16 Gene

snoRNA

Aliases for SCARNA16 Gene

External Ids for SCARNA16 Gene

Previous GeneCards Identifiers for SCARNA16 Gene

  • GC17P072601
  • GC17P072602
  • GC17P072605
  • GC17P075085
  • GC17P077090
  • GC17P077091
  • GC17P077096
  • GC17P077097
  • GC17P077099
  • GC17P077103
  • GC17P077092

Summaries for SCARNA16 Gene

GeneCards Summary for SCARNA16 Gene

SCARNA16 (Small Cajal Body-Specific RNA 16) is an RNA Gene, and is affiliated with the snoRNA class. Diseases associated with SCARNA16 include Presbyopia and Eye Accommodation Disease.

Rfam classification for SCARNA16 Gene

  • Small Cajal body specific RNA 16

Additional gene information for SCARNA16 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 SCARNA16 Gene

Genomics for SCARNA16 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCARNA16 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
GH17J077087 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 -0.2 -180 3.9 TBP MXD4 SP1 CEBPA NR2C1 DEK MNT SMAD5 ETS1 ZNF217 MIR6516 SCARNA16 SEC14L1 SRSF2 SEPTIN9 METTL23 ENSG00000267546 MFSD11 ENSG00000272386 SNHG20
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCARNA16 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the SCARNA16 gene promoter:
  • AREB6
  • c-Ets-1
  • c-Myc
  • FOXJ2
  • FOXJ2 (long isoform)
  • HSF2
  • Max1
  • Nkx2-5
  • Pax-4a
  • USF-1

Genomic Locations for SCARNA16 Gene

Latest Assembly
chr17:77,089,307-77,089,493
(GRCh38/hg38)
Size:
187 bases
Orientation:
Plus strand

Previous Assembly
chr17:75,085,389-75,085,575
(GRCh37/hg19 by Entrez Gene)
Size:
187 bases
Orientation:
Plus strand

Genomic View for SCARNA16 Gene

Genes around SCARNA16 on UCSC Golden Path with GeneCards custom track
SCARNA16 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
SCARNA16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA16 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA16 Gene

Proteins for SCARNA16 Gene

Post-translational modifications for SCARNA16 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA16 Gene

Domains & Families for SCARNA16 Gene

Gene Families for SCARNA16 Gene

genes like me logo Genes that share domains with SCARNA16: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SCARNA16 Gene

Function for SCARNA16 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 SCARNA16 Gene

Localization for SCARNA16 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 SCARNA16 gene
Compartment Confidence
nucleus 1

Gene Ontology (GO) - Cellular Components for SCARNA16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with SCARNA16: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for SCARNA16 Gene

Pathways & Interactions for SCARNA16 Gene

PathCards logo

SuperPathways for SCARNA16 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCARNA16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SCARNA16: view

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for SCARNA16 Gene

Drugs & Compounds for SCARNA16 Gene

No Compound Related Data Available

Transcripts for SCARNA16 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for SCARNA16 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000015F227_9606 snoRNA 187 6

RefSeq: NR_003013,

Ensembl: ENST00000515981 (view in UCSC) ,

Rfam: RF00424,

snoDB: SNODB54,

snOPY: Homo_sapiens300772,

ENA: AJ609486.1:1..187:ncRNA,

URS0001BC939F_9606 snoRNA 187 1

Rfam: RF00424,

SCARNA16 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for SCARNA16 Gene

1 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA16 Gene

No ASD Table

Relevant External Links for SCARNA16 Gene

GeneLoc Exon Structure for
SCARNA16

Expression for SCARNA16 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCARNA16 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCARNA16

genes like me logo Genes that share expression patterns with SCARNA16: 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 SCARNA16 Gene

Orthologs for SCARNA16 Gene

Evolution for SCARNA16 Gene

ENSEMBL:
Gene Tree for SCARNA16 (if available)
TreeFam:
Gene Tree for SCARNA16 (if available)

No data available for Orthologs for SCARNA16 Gene

Paralogs for SCARNA16 Gene

No data available for Paralogs for SCARNA16 Gene

Variants for SCARNA16 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SCARNA16 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 SCARNA16 Gene

Variant ID Type Subtype PubMed ID
dgv5784n54 CNV gain 21841781
esv3582914 CNV loss 25503493
esv3641304 CNV gain 21293372

Additional Variant Information for SCARNA16 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA16

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 SCARNA16 Gene

Disorders for SCARNA16 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SCARNA16 Gene - From: COP

Disorder Aliases PubMed IDs
presbyopia
eye accommodation disease
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCARNA16

genes like me logo Genes that share disorders with SCARNA16: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCARNA16 Gene

Publications for SCARNA16 Gene

  1. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. (PMID: 22658674) Castello A … Hentze MW (Cell 2012) 3
  2. Human box H/ACA pseudouridylation guide RNA machinery. (PMID: 15199136) Kiss AM … Kiss T (Molecular and cellular biology 2004) 3

Products for SCARNA16 Gene

Sources for SCARNA16 Gene