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

Aliases for SCARNA6 Gene

Subcategory (RNA class) for SCARNA6 Gene

non-coding RNA

Quality Score for this RNA gene is

3

Aliases for SCARNA6 Gene

  • Small Cajal Body-Specific RNA 6 2 3 5
  • U88 3

External Ids for SCARNA6 Gene

Previous GeneCards Identifiers for SCARNA6 Gene

  • GC02P233862
  • GC02P234228
  • GC02P225998
  • GC02P234246
  • GC02P234257

Summaries for SCARNA6 Gene

GeneCards Summary for SCARNA6 Gene

SCARNA6 (Small Cajal Body-Specific RNA 6) is an RNA Gene, and is affiliated with the non-coding RNA class. Diseases associated with SCARNA6 include Atrioventricular Septal Defect.

Additional gene information for SCARNA6 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 SCARNA6 Gene

Genomics for SCARNA6 Gene

GeneHancer (GH) Regulatory Elements for SCARNA6 Gene

Promoters and enhancers for SCARNA6 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
GH02I233288 Enhancer 0.6 ENCODE 550.8 +0.3 274 0.2 SMARCE1 PKNOX1 ESRRA FOXA2 FOXA1 ZNF217 GATA3 CUX1 FOS GC02P233297 GC02P233298 PIR49212 SCARNA6 GC02P233300 GC02M233297 ATG16L1
GH02I233565 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 19.4 +277.7 277688 2.1 PKNOX1 SMAD1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 USP40 SCARNA6 GIGYF2 ATG16L1 LOC100422710
GH02I233348 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 +65.7 65698 11.5 HDGF FOXA2 PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 DGKD ENSG00000259793 ATG16L1 USP40 SAG SCARNA5 GIGYF2 SCARNA6 INPP5D
GH02I234145 Enhancer 1.1 Ensembl ENCODE dbSUPER 23.8 +858.6 858550 2.5 JUN ZFP64 ZNF140 FEZF1 ZIC2 ZNF697 POLR2A ZNF433 TCF7L2 ZBTB11 SCARNA6 USP40 ARL4C ATG16L1 ENSG00000226442 LOC105373932
GH02I232696 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10.1 -590.4 -590392 3.7 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF207 ZNF143 GIGYF2 RPL28P2 DIS3L2 USP40 SCARNA6 COPS7B ATG16L1 NGEF SNORC GC02P232728
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCARNA6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCARNA6 gene promoter:

Genomic Locations for SCARNA6 Gene

Genomic Locations for SCARNA6 Gene
chr2:233,288,676-233,288,941
(GRCh38/hg38)
Size:
266 bases
Orientation:
Plus strand
chr2:234,197,322-234,197,587
(GRCh37/hg19)

Genomic View for SCARNA6 Gene

Genes around SCARNA6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARNA6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA6 Gene

Proteins for SCARNA6 Gene

Post-translational modifications for SCARNA6 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA6 Gene

Domains & Families for SCARNA6 Gene

Gene Families for SCARNA6 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCARNA6: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SCARNA6 Gene

Function for SCARNA6 Gene

Phenotypes From GWAS Catalog for SCARNA6 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 SCARNA6 Gene

Localization for SCARNA6 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 SCARNA6 Gene

Pathways & Interactions for SCARNA6 Gene

SuperPathways for SCARNA6 Gene

No Data Available

Interacting Proteins for SCARNA6 Gene

Gene Ontology (GO) - Biological Process for SCARNA6 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SCARNA6 Gene

Drugs & Compounds for SCARNA6 Gene

No Compound Related Data Available

Transcripts for SCARNA6 Gene

mRNA/cDNA for SCARNA6 Gene

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

Unigene Clusters for SCARNA6 Gene

Small Cajal body-specific RNA 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA6 Gene

No ASD Table

Relevant External Links for SCARNA6 Gene

GeneLoc Exon Structure for
SCARNA6
ECgene alternative splicing isoforms for
SCARNA6

Expression for SCARNA6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCARNA6 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCARNA6 Gene:

SCARNA6

SOURCE GeneReport for Unigene cluster for SCARNA6 Gene:

Hs.689637
genes like me logo Genes that share expression patterns with SCARNA6: 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 SCARNA6 Gene

Orthologs for SCARNA6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCARNA6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCARNA6 34
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Scarna6 34
  • 78 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SCARNA6 34
  • 73 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SCARNA6 34
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCARNA6 34
  • 64 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCARNA6 34
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCARNA6 34
  • 56 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia SCARNA6 34
  • 58 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii SCARNA6 34
  • 47 (a)
ManyToMany
Species where no ortholog for SCARNA6 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 SCARNA6 Gene

ENSEMBL:
Gene Tree for SCARNA6 (if available)
TreeFam:
Gene Tree for SCARNA6 (if available)

Paralogs for SCARNA6 Gene

No data available for Paralogs for SCARNA6 Gene

Variants for SCARNA6 Gene

Sequence variations from dbSNP and Humsavar for SCARNA6 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000563098 -- 233,288,329(+) T/C upstream_transcript_variant
rs1001503998 -- 233,287,947(+) A/G upstream_transcript_variant
rs1004549748 -- 233,287,519(+) A/G upstream_transcript_variant
rs1007895767 -- 233,289,283(+) C/T downstream_transcript_variant
rs1010984280 -- 233,287,183(+) C/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SCARNA6 Gene

Variant ID Type Subtype PubMed ID
nsv584699 CNV gain 21841781

Additional Variant Information for SCARNA6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SCARNA6 Gene

Disorders for SCARNA6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCARNA6 Gene - From: DISEASES

Disorder Aliases PubMed IDs
atrioventricular septal defect
  • avsd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCARNA6

genes like me logo Genes that share disorders with SCARNA6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCARNA6 Gene

Publications for SCARNA6 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

Products for SCARNA6 Gene

Sources for SCARNA6 Gene

Content
Loading form....