Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SCARNA5 Gene

Subcategory (RNA class) for SCARNA5 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for SCARNA5 Gene

  • Small Cajal Body-Specific RNA 5 2 3 5
  • U87 3

External Ids for SCARNA5 Gene

Previous GeneCards Identifiers for SCARNA5 Gene

  • GC02P233849
  • GC02P234184
  • GC02P225985

Summaries for SCARNA5 Gene

GeneCards Summary for SCARNA5 Gene

SCARNA5 (Small Cajal Body-Specific RNA 5) is an RNA Gene, and is affiliated with the non-coding RNA class.

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCARNA5 Gene

Genomics for SCARNA5 Gene

Regulatory Elements for SCARNA5 Gene

Enhancers for SCARNA5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F233412 1.6 FANTOM5 Ensembl ENCODE 10.1 +146.0 146048 18.4 PKNOX1 ATF1 ARNT SIN3A GLIS2 CBX5 FOS REST TBX21 MBD2 USP40 SAG ATG16L1 DGKD SCARNA6 SCARNA5 LOC105373929 INPP5D PIR59405 GC02M233380
GH02F233383 1.2 Ensembl ENCODE 10.5 +110.9 110911 5.7 MLX ARID4B DMAP1 ZNF48 YY1 SP5 NFYC MXD4 MIER2 REST DGKD ATG16L1 USP40 SAG SCARNA5 SCARNA6 ENSG00000201013 GC02M233380 PIR59405
GH02F232855 1.3 Ensembl ENCODE 9.6 -417.1 -417122 6.8 ATF1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 NFYC ZHX2 MXD4 C2orf82 NGEF ATG16L1 SCARNA5 PIR45244
GH02F233329 1.1 Ensembl ENCODE 10.5 +56.7 56675 6.0 SIN3A ZBTB40 ZNF366 ETV6 FOS CREM TBX21 NR2F2 GLIS1 IKZF1 SAG DGKD ATG16L1 SCARNA6 SCARNA5 ENSG00000259793
GH02F233239 1 Ensembl ENCODE 11.3 -33.5 -33526 6.4 KLF1 ZNF133 FEZF1 ZIC2 NR2F6 ETV6 MAFK TCF7L2 MTA2 NRF1 ATG16L1 ENSG00000251485 SCARNA5 USP40 GC02P233277
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCARNA5 on UCSC Golden Path with GeneCards custom track

Genomic Location for SCARNA5 Gene

233,275,726 bp from pter
233,276,003 bp from pter
278 bases
Plus strand

Genomic View for SCARNA5 Gene

Genes around SCARNA5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARNA5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA5 Gene

Proteins for SCARNA5 Gene

Post-translational modifications for SCARNA5 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA5 Gene

Domains & Families for SCARNA5 Gene

Gene Families for SCARNA5 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCARNA5: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SCARNA5 Gene

Function for SCARNA5 Gene

Animal Model 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 SCARNA5 Gene

Localization for SCARNA5 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for SCARNA5 Gene

Pathways & Interactions for SCARNA5 Gene

SuperPathways for SCARNA5 Gene

No Data Available

Interacting Proteins for SCARNA5 Gene

Gene Ontology (GO) - Biological Process for SCARNA5 Gene


No data available for Pathways by source and SIGNOR curated interactions for SCARNA5 Gene

Transcripts for SCARNA5 Gene

mRNA/cDNA for SCARNA5 Gene

(1) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SCARNA5 Gene

Small Cajal body-specific RNA 5:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA5 Gene

No ASD Table

Relevant External Links for SCARNA5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCARNA5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCARNA5 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCARNA5 Gene:


SOURCE GeneReport for Unigene cluster for SCARNA5 Gene:

genes like me logo Genes that share expression patterns with SCARNA5: 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 and mRNA Expression by UniProt/SwissProt for SCARNA5 Gene

Orthologs for SCARNA5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCARNA5 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCARNA6 35
  • 100 (a)
(Bos Taurus)
Mammalia SCARNA6 35
  • 84 (a)
(Canis familiaris)
Mammalia SCARNA6 35
  • 81 (a)
(Mus musculus)
Mammalia Gm25395 35
  • 75 (a)
(Monodelphis domestica)
Mammalia SCARNA6 35
  • 60 (a)
(Ornithorhynchus anatinus)
Mammalia SCARNA6 35 35
  • 55 (a)
(Gallus gallus)
Aves SCARNA6 35
  • 55 (a)
(Anolis carolinensis)
Reptilia SCARNA6 35
  • 58 (a)
(Danio rerio)
Actinopterygii SCARNA6 35
  • 52 (a)
Species where no ortholog for SCARNA5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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 SCARNA5 Gene

Gene Tree for SCARNA5 (if available)
Gene Tree for SCARNA5 (if available)

Paralogs for SCARNA5 Gene

No data available for Paralogs for SCARNA5 Gene

Variants for SCARNA5 Gene

Sequence variations from dbSNP and Humsavar for SCARNA5 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs2241880 other 233,274,722(-) ATGAG(C/T)ATCCA nc-transcript-variant, upstream-variant-2KB, reference, missense
rs111551898 -- 233,274,918(+) TGTCA(A/G)CTGTG intron-variant, upstream-variant-2KB
rs111819481 -- 233,274,510(+) GTGCT(A/T)TTGAT intron-variant, upstream-variant-2KB
rs112046982 -- 233,274,843(+) TAAAG(C/G)GTCCT intron-variant, upstream-variant-2KB
rs112572627 -- 233,274,679(+) AGGAG(A/G)CGCTC nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for SCARNA5 Gene

Variant ID Type Subtype PubMed ID
nsv584699 CNV gain 21841781

Relevant External Links for SCARNA5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SCARNA5 Gene

Disorders for SCARNA5 Gene

Relevant External Links for SCARNA5

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SCARNA5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCARNA5 Gene

Publications for SCARNA5 Gene

  1. Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs. (PMID: 12032087) Darzacq X. … Kiss T. (EMBO J. 2002) 2 3 64
  2. A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300. (PMID: 22936669) JuliA A. … Marsal S. (Gut 2013) 3 64
  3. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. (PMID: 22412388) Kenny E.E. … Peter I. (PLoS Genet. 2012) 3 64
  4. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. (PMID: 22658674) Castello A. … Hentze M.W. (Cell 2012) 3 64
  5. Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. (PMID: 20570966) McGovern D.P. … Rotter J.I. (Hum. Mol. Genet. 2010) 3 64

Products for SCARNA5 Gene

Sources for SCARNA5 Gene

Loading form....