Aliases for SCARNA4 Gene

Subcategory (RNA class) for SCARNA4 Gene

snoRNA

Number of RNA Genes sources:

4 / 17

Aliases for SCARNA4 Gene

  • Small Cajal Body-Specific RNA 4 2 3 5
  • SCARNA4 2 5 170
  • ACA26 2 3
  • ACA26 ScaRNA 3
  • SNODB1166 177
  • SNODB232 177
  • RF00426 168
  • RF00423 168

External Ids for SCARNA4 Gene

Additional External Ids for SCARNA4 Gene

Previous GeneCards Identifiers for SCARNA4 Gene

  • GC01M154162
  • GC01M155895
  • GC01M127256

Summaries for SCARNA4 Gene

GeneCards Summary for SCARNA4 Gene

SCARNA4 (Small Cajal Body-Specific RNA 4) is an RNA Gene, and is affiliated with the snoRNA class.

Rfam classification for SCARNA4 Gene

  • Small Cajal body specific RNA 4

Additional gene information for SCARNA4 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 SCARNA4 Gene

Genomics for SCARNA4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCARNA4 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
GH01J155965 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 12 -49.3 -49291 19 ARHGAP35 HNRNPL GATAD2A CTCF TEAD4 PRDM10 ZNF629 TFE3 LEF1 IKZF1 ARHGEF2 RIT1 KHDC4 GON4L CLK2 PAQR6 PRCC RRNAD1 YY1AP1 ENSG00000271267
GH01J156000 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 11.6 -76.4 -76392 3.6 GATAD2A PRDM10 IKZF1 ZNF692 JUND FOXA1 MTA2 RFX1 ZSCAN4 RXRB ENSG00000285677 LOC107985208 RIT1 RXFP4 KHDC4 LAMTOR2 UBQLN4 SCARNA4 MEX3A LMNA
GH01J155958 Enhancer 1.2 Ensembl ENCODE dbSUPER 12.1 -35.5 -35474 5.3 HNRNPL ZNF629 CTCF ZIC2 REST IKZF2 ZNF600 EED SP1 DPF2 RIT1 ARHGEF2-AS1 ARHGEF2 KHDC4 SCARNA4 LAMTOR2 UBQLN4 ENSG00000273002 SSR2 MIR6738
GH01J155949 Enhancer 0.6 dbSUPER 12.4 -25.5 -25549 3.6 RELA RBFOX2 PKNOX1 POLR2A GABPA RBM22 SPI1 EBF1 MEIS2 GABPB1 MIR6738 RIT1 SCARNA4 ARHGEF2-AS1 ARHGEF2 SNORA80E UBQLN4 LAMTOR2 LMNA MEX3A
GH01J156004 Enhancer 0.6 ENCODE dbSUPER 11.6 -79.2 -79158 1.2 ZBTB17 EGR2 SP5 ARHGEF2 lnc-ARHGEF2-1 RXFP4 KHDC4 UBQLN4 LAMTOR2 SCARNA4 RIT1 LMNA MEX3A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCARNA4 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the SCARNA4 gene promoter:
  • AP-4
  • AREB6
  • ATF6
  • CREB
  • CUTL1
  • deltaCREB
  • NF-1
  • NF-1/L
  • Pax-4a
  • POU3F1

Genomic Locations for SCARNA4 Gene

Genomic Locations for SCARNA4 Gene
chr1:155,925,958-155,926,086
(GRCh38/hg38)
Size:
129 bases
Orientation:
Minus strand
chr1:155,895,749-155,895,877
(GRCh37/hg19)
Size:
129 bases
Orientation:
Minus strand

Genomic View for SCARNA4 Gene

Genes around SCARNA4 on UCSC Golden Path with GeneCards custom track
SCARNA4 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
SCARNA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA4 Gene

Proteins for SCARNA4 Gene

Post-translational modifications for SCARNA4 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA4 Gene

Domains & Families for SCARNA4 Gene

Gene Families for SCARNA4 Gene

genes like me logo Genes that share domains with SCARNA4: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SCARNA4 Gene

Function for SCARNA4 Gene

Phenotypes From GWAS Catalog for SCARNA4 Gene

Animal Model Products

CRISPR Products

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 SCARNA4 Gene

Localization for SCARNA4 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 SCARNA4 gene
Compartment Confidence
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SCARNA4 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 SCARNA4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for SCARNA4 Gene

Pathways & Interactions for SCARNA4 Gene

PathCards logo

SuperPathways for SCARNA4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCARNA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SCARNA4: view

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for SCARNA4 Gene

Drugs & Compounds for SCARNA4 Gene

No Compound Related Data Available

Transcripts for SCARNA4 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for SCARNA4 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS00005C0742_9606 snoRNA 129 7

HGNC: 32560,

RefSeq: NR_003005,

Ensembl: ENST00000625402 (view in UCSC) ,

Rfam: RF00423,

snoDB: SNODB232,

snOPY: Homo_sapiens300780,

ENA: AJ609483.1:1..129:ncRNA,

URS000071234F_9606 snoRNA 128 3

Ensembl: ENST00000629045 (view in UCSC) ,

Rfam: RF00426,

snoDB: SNODB1166,

SCARNA4 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for SCARNA4 Gene

1 NCBI additional mRNA sequence :

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA4 Gene

No ASD Table

Relevant External Links for SCARNA4 Gene

GeneLoc Exon Structure for
SCARNA4

Expression for SCARNA4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCARNA4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCARNA4

SOURCE GeneReport for Unigene cluster for SCARNA4 Gene:

Hs.678903
genes like me logo Genes that share expression patterns with SCARNA4: 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 SCARNA4 Gene

Orthologs for SCARNA4 Gene

Evolution for SCARNA4 Gene

ENSEMBL:
Gene Tree for SCARNA4 (if available)
TreeFam:
Gene Tree for SCARNA4 (if available)

No data available for Orthologs for SCARNA4 Gene

Paralogs for SCARNA4 Gene

No data available for Paralogs for SCARNA4 Gene

Variants for SCARNA4 Gene

Additional dbSNP identifiers (rs#s) for SCARNA4 Gene

Structural Variations from Database of Genomic Variants (DGV) for SCARNA4 Gene

Variant ID Type Subtype PubMed ID
esv33869 CNV loss 17666407

Additional Variant Information for SCARNA4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA4

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 SCARNA4 Gene

Disorders for SCARNA4 Gene

Additional Disease Information for SCARNA4

No disorders were found for SCARNA4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCARNA4 Gene

Publications for SCARNA4 Gene

  1. Human box H/ACA pseudouridylation guide RNA machinery. (PMID: 15199136) Kiss AM … Kiss T (Molecular and cellular biology 2004) 3
  2. A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs. (PMID: 12912925) Richard P … Kiss T (The EMBO journal 2003) 3
  3. 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 SCARNA4 Gene

Sources for SCARNA4 Gene