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Aliases for SCARNA1 Gene

Subcategory (RNA class) for SCARNA1 Gene

scaRNA

Quality Score for this RNA gene is

3

Aliases for SCARNA1 Gene

  • Small Cajal Body-Specific RNA 1 2 3 5
  • ACA35 ScaRNA 3
  • ACA35 3

External Ids for SCARNA1 Gene

Previous GeneCards Identifiers for SCARNA1 Gene

  • GC01P028033
  • GC01P028161
  • GC01P026417
  • GC01P028164
  • GC01P028168

Summaries for SCARNA1 Gene

GeneCards Summary for SCARNA1 Gene

SCARNA1 (Small Cajal Body-Specific RNA 1) is an RNA Gene, and is affiliated with the scaRNA class.

Additional gene information for SCARNA1 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 SCARNA1 Gene

Genomics for SCARNA1 Gene

GeneHancer (GH) Regulatory Elements for SCARNA1 Gene

Promoters and enhancers for SCARNA1 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
GH01I027871 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11 +40.2 40223 5.3 HDGF PKNOX1 ATF1 SMAD1 FEZF1 IRF4 GTF3C2 POLR2B ZNF207 ZNF143 THEMIS2 FGR RPA2 XKR8 EYA3 PTAFR PPP1R8 SCARNA1 RNU6-1245P SESN2
GH01I027771 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 11.7 -61.0 -61036 3.4 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF213 STX12 ENSG00000269971 GMEB1 ACTG1P20 RNU6-1245P PPP1R8 SCARNA1 FAM76A ENSG00000231344 PHACTR4
GH01I027881 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.8 +53.4 53410 11.7 HDGF PKNOX1 BATF KLF5 IRF4 RARA SCRT2 ZNF143 ATF7 ETV6 RPA2 XKR8 THEMIS2 SMPDL3B ENSG00000227050 EYA3 SCARNA1 PPP1R8 RNU6-1245P FGR
GH01I028110 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.3 +278.2 278200 4.4 HDGF PKNOX1 ATF1 ARNT ZFP64 ZNF766 FOS ATF7 RUNX3 NCOA1 PTAFR EYA3 SNHG12 FGR GMEB1 ACTG1P20 TRNAU1AP RNU6-176P RNU7-29P PHACTR4
GH01I027425 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.3 -401.6 -401619 13.6 HDGF PKNOX1 ATF1 FOXA2 ARNT ETS1 TCF12 ZNF766 E2F8 ARID2 ACTG1P20 CD164L2 WASF2 FGR LOC105376892 ARID1A FAM76A RNU6-48P TMEM222 PHACTR4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCARNA1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCARNA1 gene promoter:

Genomic Locations for SCARNA1 Gene

Genomic Locations for SCARNA1 Gene
chr1:27,834,401-27,834,566
(GRCh38/hg38)
Size:
166 bases
Orientation:
Plus strand
chr1:28,160,912-28,161,077
(GRCh37/hg19)

Genomic View for SCARNA1 Gene

Genes around SCARNA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARNA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA1 Gene

Proteins for SCARNA1 Gene

Post-translational modifications for SCARNA1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA1 Gene

Domains & Families for SCARNA1 Gene

Gene Families for SCARNA1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCARNA1: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SCARNA1 Gene

Function for SCARNA1 Gene

Phenotypes From GWAS Catalog for SCARNA1 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 SCARNA1 Gene

Localization for SCARNA1 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 SCARNA1 Gene

Pathways & Interactions for SCARNA1 Gene

SuperPathways for SCARNA1 Gene

No Data Available

Interacting Proteins for SCARNA1 Gene

Gene Ontology (GO) - Biological Process for SCARNA1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SCARNA1 Gene

Drugs & Compounds for SCARNA1 Gene

No Compound Related Data Available

Transcripts for SCARNA1 Gene

mRNA/cDNA for SCARNA1 Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA1 Gene

No ASD Table

Relevant External Links for SCARNA1 Gene

GeneLoc Exon Structure for
SCARNA1
ECgene alternative splicing isoforms for
SCARNA1

Expression for SCARNA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCARNA1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCARNA1 Gene:

SCARNA1

SOURCE GeneReport for Unigene cluster for SCARNA1 Gene:

Hs.689694
genes like me logo Genes that share expression patterns with SCARNA1: 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 SCARNA1 Gene

Orthologs for SCARNA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCARNA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCARNA1 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SCARNA1 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SCARNA1 34
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gm22767 34
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCARNA1 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCARNA1 34 34 34 34
  • 71 (a)
OneToMany
chicken
(Gallus gallus)
Aves SCARNA1 34
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCARNA1 34
  • 66 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii SCARNA1 34
  • 54 (a)
OneToOne
Species where no ortholog for SCARNA1 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 SCARNA1 Gene

ENSEMBL:
Gene Tree for SCARNA1 (if available)
TreeFam:
Gene Tree for SCARNA1 (if available)

Paralogs for SCARNA1 Gene

No data available for Paralogs for SCARNA1 Gene

Variants for SCARNA1 Gene

Sequence variations from dbSNP and Humsavar for SCARNA1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000658436 -- 27,834,077(+) A/G upstream_transcript_variant
rs1000766647 -- 27,835,008(+) A/T downstream_transcript_variant
rs1006337061 -- 27,833,425(+) A/G upstream_transcript_variant
rs1009928708 -- 27,834,042(+) T/A upstream_transcript_variant
rs1011554850 -- 27,834,197(+) A/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SCARNA1 Gene

Variant ID Type Subtype PubMed ID
nsv509069 CNV insertion 20534489

Additional Variant Information for SCARNA1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SCARNA1 Gene

Disorders for SCARNA1 Gene

Additional Disease Information for SCARNA1

No disorders were found for SCARNA1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCARNA1 Gene

Publications for SCARNA1 Gene

  1. Human box H/ACA pseudouridylation guide RNA machinery. (PMID: 15199136) Kiss AM … Kiss T (Molecular and cellular biology 2004) 3 58

Products for SCARNA1 Gene

Sources for SCARNA1 Gene

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