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SCARNA5 Gene(RNA Gene)

Small Cajal Body-Specific RNA 5

GCID:
GC02P233275
GIFtS:
17
Genes Participants
UDN Logo

Aliases for SCARNA5 Gene

Subcategory (RNA class) for SCARNA5 Gene

non-coding RNA

Quality Score for this RNA gene is

3

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.

Additional gene information for SCARNA5 Gene

No data available for Entrez Gene Summary , CIViC 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

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for SCARNA5 Gene

Promoters and enhancers for SCARNA5 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
GH02I233348 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.3 +78.6 78648 11.5 HDGF FOXA2 PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 DGKD ENSG00000259793 ATG16L1 USP40 SAG SCARNA5 GIGYF2 SCARNA6 INPP5D
GH02I233384 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 10.5 +111.1 111071 5.3 FOXA2 MLX ARID4B DMAP1 ZNF48 YY1 RUNX3 RXRA SP5 NFYC DGKD ATG16L1 USP40 SAG SCARNA5 SCARNA6 ENSG00000201013 GC02M233380 PIR59405
GH02I233412 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.1 +146.0 146047 18.4 PKNOX1 CLOCK FOXA2 ARNT SIN3A FOS KLF13 REST ZNF592 SMARCA4 USP40 SAG ATG16L1 DGKD SCARNA6 SCARNA5 INPP5D LOC105373929 PIR59405 GC02M233380
GH02I232872 Promoter/Enhancer 1.5 Ensembl ENCODE dbSUPER 9.5 -400.4 -400365 4.9 DRAP1 ELF3 CTCF MXI1 SAP130 SUZ12 ARID4B SIN3A BACH1 DMAP1 SNORC NGEF GIGYF2 LOC101928881 KCNJ13 ATG16L1 SCARNA5 PIR45244
GH02I233330 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.5 +56.8 56820 3.2 MAX ZBTB40 IRF4 POLR2A ZNF143 ATF7 ETV6 IKZF2 RUNX3 SRF DGKD ATG16L1 SAG SCARNA6 SCARNA5 ENSG00000259793
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCARNA5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCARNA5 gene promoter:

Genomic Locations for SCARNA5 Gene

Genomic Locations for SCARNA5 Gene
chr2:233,275,726-233,276,003
(GRCh38/hg38)
Size:
278 bases
Orientation:
Plus strand
chr2:234,184,372-234,184,649
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for SCARNA5 Gene

Proteins for SCARNA5 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

HGNC:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes From GWAS Catalog for SCARNA5 Gene

Animal Model Products

Clone 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 , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for SCARNA5 Gene

Pathways & Interactions for SCARNA5 Gene

SuperPathways for SCARNA5 Gene

PathCards logo More details on SuperPathways for SCARNA5
No Data Available

Interacting Proteins for SCARNA5 Gene

Gene Ontology (GO) - Biological Process for SCARNA5 Gene

None

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

Drugs & Compounds for SCARNA5 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SCARNA5 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

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:

Clone Products

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

No ASD Table

Relevant External Links for SCARNA5 Gene

GeneLoc Exon Structure for
SCARNA5
ECgene alternative splicing isoforms for
SCARNA5

Expression for SCARNA5 Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for SCARNA5 Gene
mRNA expression by GTEx for SCARNA5 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCARNA5 Gene:

SCARNA5

SOURCE GeneReport for Unigene cluster for SCARNA5 Gene:

Hs.663619
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 , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
 Mammalia SCARNA6 34
  • 100 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia SCARNA6 34
  • 84 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia SCARNA6 34
  • 81 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Gm25395 34
  • 75 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia SCARNA6 34
  • 60 (a)
 OneToMany
platypus
(Ornithorhynchus anatinus)
 Mammalia SCARNA6 34 34
  • 55 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves SCARNA6 34
  • 55 (a)
 OneToMany
lizard
(Anolis carolinensis)
 Reptilia SCARNA6 34
  • 58 (a)
 OneToMany
zebrafish
(Danio rerio)
 Actinopterygii SCARNA6 34
  • 52 (a)
 ManyToMany
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

ENSEMBL:
Gene Tree for SCARNA5 (if available)
TreeFam:
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 Variation AA Info Type
rs2241880 risk-factor, benign, Inflammatory bowel disease 10, susceptibility to, not specified 233,274,722(+) A/G upstream_transcript_variant
rs1000814412 -- 233,275,575(+) T/C upstream_transcript_variant
rs1001099583 -- 233,275,203(+) G/A upstream_transcript_variant
rs1001987388 -- 233,275,915(+) G/A non_coding_transcript_variant
rs1002014188 -- 233,273,868(+) G/T upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
nsv584699 CNV gain 21841781

Additional Variant Information for SCARNA5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA5

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

Disorders for SCARNA5 Gene

Additional Disease Information 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 (The EMBO journal 2002) 2 3 58
  2. A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300. (PMID: 22936669) Julià A … Marsal S (Gut 2013) 3 58
  3. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. (PMID: 22412388) Kenny EE … Peter I (PLoS genetics 2012) 3 58
  4. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. (PMID: 22658674) Castello A … Hentze MW (Cell 2012) 3 58
  5. Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. (PMID: 20570966) McGovern DP … International IBD Genetics Consortium (Human molecular genetics 2010) 3 58

Products for SCARNA5 Gene

Sources for SCARNA5 Gene

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