Aliases for SCARNA9 Gene

Subcategory (RNA class) for SCARNA9 Gene


Quality Score for this RNA gene is


Aliases for SCARNA9 Gene

  • Small Cajal Body-Specific RNA 9 2 3 5
  • MgU2-19/30 ScaRNA 3
  • Lnc-C11orf54-1 170
  • NONHSAG009372 94
  • MgU2-19/30 3
  • SCARNA9 2
  • Z32 3

External Ids for SCARNA9 Gene

Previous GeneCards Identifiers for SCARNA9 Gene

  • GC11P093098
  • GC11P093456
  • GC11P089531
  • GC11P093457
  • GC11P093458
  • GC11P093459
  • GC11P093460
  • GC11P093462
  • GC11P093466
  • GC11P093479
  • GC11P093723
  • GC11P093725
  • GC11P093748
  • GC11P093752
  • GC11P093728
  • GC11P093730
  • GC11P093732
  • GC11P093734
  • GC11P093736
  • GC11P093738
  • GC11P093740
  • GC11P093746

Summaries for SCARNA9 Gene

GeneCards Summary for SCARNA9 Gene

SCARNA9 (Small Cajal Body-Specific RNA 9) is an RNA Gene, and is affiliated with the lncRNA class.

Rfam classification for SCARNA9 Gene

Additional gene information for SCARNA9 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 SCARNA9 Gene

Genomics for SCARNA9 Gene

GeneHancer (GH) Regulatory Elements for SCARNA9 Gene

Promoters and enhancers for SCARNA9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J094127 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.1 +411.0 410972 10.4 SIN3A ZBTB40 ZBTB6 SMARCE1 POLR2A TCF7L2 USF2 CREB1 MYC CC2D1A PANX1 MED17 CEP295 ENSG00000255445 SNORA1 HEPHL1 MRE11 ENSG00000255893 SCARNA9 ANKRD49
GH11J093688 Enhancer 0.4 Ensembl 11.3 -31.9 -31913 1.6 SCRT2 BATF EBF1 CEP295 C11orf54 SNORA1 SNORA25 SNORA32 SNORD6 ENSG00000199875 SCARNA9 TAF1D SNORA18
GH11J094673 Enhancer 0.7 Ensembl ENCODE 4.8 +955.1 955136 6.7 NR2C1 RFX1 CTBP1 NR2C2 FOSL1 GATA3 CBFA2T3 AMOTL1 ENSG00000255929 ENSG00000256469 SCARNA9 ENSG00000255893 ENSG00000250519 piR-44343 LOC105369438
GH11J094664 Enhancer 0.4 Ensembl ENCODE 5.2 +943.4 943388 1.8 POLR2A SCARNA9 piR-44343 piR-30444-058 ENSG00000255929 LOC105369438
GH11J094661 Enhancer 0.5 Ensembl ENCODE 4.4 +940.6 940588 0.6 SP1 RUNX3 SCARNA9 piR-44343 piR-30444-058 ENSG00000255929 LOC105369438
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCARNA9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCARNA9 gene promoter:
  • aMEF-2
  • AML1a
  • Evi-1
  • GATA-1
  • ITF-2
  • MEF-2A
  • POU2F1
  • POU2F1a
  • RORalpha1
  • Tal-1beta

Genomic Locations for SCARNA9 Gene

Genomic Locations for SCARNA9 Gene
354 bases
Plus strand
354 bases
Plus strand

Genomic View for SCARNA9 Gene

Genes around SCARNA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARNA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA9 Gene

Proteins for SCARNA9 Gene

Post-translational modifications for SCARNA9 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA9 Gene

Domains & Families for SCARNA9 Gene

Gene Families for SCARNA9 Gene

genes like me logo Genes that share domains with SCARNA9: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SCARNA9 Gene

Function for SCARNA9 Gene

Phenotypes From GWAS Catalog for SCARNA9 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 SCARNA9 Gene

Localization for SCARNA9 Gene

Gene Ontology (GO) - Cellular Components for SCARNA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with SCARNA9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for SCARNA9 Gene

Pathways & Interactions for SCARNA9 Gene

PathCards logo

SuperPathways for SCARNA9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCARNA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SCARNA9: view

No data available for Pathways by source and SIGNOR curated interactions for SCARNA9 Gene

Drugs & Compounds for SCARNA9 Gene

No Compound Related Data Available

Transcripts for SCARNA9 Gene

mRNA/cDNA for SCARNA9 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
(1) NONCODE transcripts :
(4) RNACentral transcripts :
(1) ENA transcripts :
(2) LNCipedia transcripts :

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA9 Gene

No ASD Table

Relevant External Links for SCARNA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCARNA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCARNA9 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCARNA9 Gene:

genes like me logo Genes that share expression patterns with SCARNA9: 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 SCARNA9 Gene

Orthologs for SCARNA9 Gene

Evolution for SCARNA9 Gene

Gene Tree for SCARNA9 (if available)
Gene Tree for SCARNA9 (if available)

No data available for Orthologs for SCARNA9 Gene

Paralogs for SCARNA9 Gene

No data available for Paralogs for SCARNA9 Gene

Variants for SCARNA9 Gene

Sequence variations from dbSNP and Humsavar for SCARNA9 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000336557 -- 93,719,557(+) C/A/T upstream_transcript_variant
rs1001387379 -- 93,719,837(+) C/G upstream_transcript_variant
rs1002527740 -- 93,720,902(+) G/A upstream_transcript_variant
rs1003432185 -- 93,720,314(+) A/C/G upstream_transcript_variant
rs1003465023 -- 93,720,163(+) G/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SCARNA9 Gene

Variant ID Type Subtype PubMed ID
esv3627294 CNV gain 21293372
nsv832232 CNV gain 17160897

Additional Variant Information for SCARNA9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SCARNA9 Gene

Disorders for SCARNA9 Gene

Additional Disease Information for SCARNA9

No disorders were found for SCARNA9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCARNA9 Gene

Publications for SCARNA9 Gene

  1. Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa. (PMID: 15556860) Tycowski KT … Steitz JA (Current biology : CB 2004) 2 3 56
  2. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 56
  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 56

Products for SCARNA9 Gene

Sources for SCARNA9 Gene