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Aliases for SCARNA12 Gene

Subcategory (RNA class) for SCARNA12 Gene


Quality Score for this RNA gene is


Aliases for SCARNA12 Gene

  • Small Cajal Body-Specific RNA 12 2 3 5
  • U89 Small Nuclear RNA 3
  • U89 3

External Ids for SCARNA12 Gene

ORGUL Members for SCARNA12 Gene

Previous GeneCards Identifiers for SCARNA12 Gene

  • GC12M006947
  • GC12M007076

Summaries for SCARNA12 Gene

Entrez Gene Summary for SCARNA12 Gene

  • This gene produces a small nuclear RNA that localizes specifically to Cajal bodies, which are conserved subnuclear organelles that are present in the nucleoplasm. This RNA is processed from an intron of the prohibitin 2 host gene. It includes both an H/ACA box and a C/D box, and is thought to guide the pseudouridylation of residue U46 in the U5 small nuclear RNA. [provided by RefSeq, Jun 2010]

GeneCards Summary for SCARNA12 Gene

SCARNA12 (Small Cajal Body-Specific RNA 12) is an RNA Gene, and is affiliated with the scaRNA class.

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCARNA12 Gene

Genomics for SCARNA12 Gene

Regulatory Elements for SCARNA12 Gene

Enhancers for SCARNA12 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
GH12G006940 1.9 FANTOM5 ENCODE dbSUPER 21.7 +13.9 13948 25.9 MLX CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SPSB2 ENSG00000219410 ENSG00000247853 NOP2 NCAPD2 SCARNA12 ENSG00000256967 ATN1 TNFRSF1A SCNN1A
GH12G006923 1.7 FANTOM5 ENCODE dbSUPER 21.9 +40.5 40456 6.8 HDGF ARID4B SIN3A ZNF2 YY1 ZNF143 FOS DEK PAF1 ZNF263 LRRC23 SCARNA12 RPL13P5 USP5 PHB2 EMG1 SPSB2 ENSG00000219410 MIR200C MIR200CHG
GH12G006546 1.8 FANTOM5 ENCODE dbSUPER 18.3 +415.7 415691 10.3 CREB3L1 AGO1 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 ENSG00000219410 ENSG00000247853 NCAPD2 TAPBPL NOP2 SCARNA12 VAMP1 SPSB2 SCARNA11 CHD4
GH12G006826 1.4 ENCODE dbSUPER 19.8 +138.9 138909 3.7 CREB3L1 MLX AGO1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC ENSG00000219410 ENSG00000247853 NOP2 SCARNA12 ENSG00000256967 NCAPD2 SPSB2 GDF3 C1RL-AS1 RPL13P5
GH12G007059 1.2 Ensembl ENCODE 21 -93.2 -93162 2.5 FOXA2 ARID4B SIN3A ZBTB7B YY1 ZNF143 ZNF416 MXD4 REST ZNF518A ENSG00000219410 ENSG00000247853 C1RL-AS1 SCARNA12 GNB3 NCAPD2 SPSB2 C1R C1RL GDF3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCARNA12 on UCSC Golden Path with GeneCards custom track

Genomic Location for SCARNA12 Gene

6,967,337 bp from pter
6,967,606 bp from pter
270 bases
Minus strand

Genomic View for SCARNA12 Gene

Genes around SCARNA12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARNA12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARNA12 Gene

Proteins for SCARNA12 Gene

Post-translational modifications for SCARNA12 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA12 Gene

Domains & Families for SCARNA12 Gene

Gene Families for SCARNA12 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCARNA12: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SCARNA12 Gene

Function for SCARNA12 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 SCARNA12 Gene

Localization for SCARNA12 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for SCARNA12 Gene

Pathways & Interactions for SCARNA12 Gene

SuperPathways for SCARNA12 Gene

No Data Available

Interacting Proteins for SCARNA12 Gene

Gene Ontology (GO) - Biological Process for SCARNA12 Gene


No data available for Pathways by source and SIGNOR curated interactions for SCARNA12 Gene

Drugs & Compounds for SCARNA12 Gene

No Compound Related Data Available

Transcripts for SCARNA12 Gene

mRNA/cDNA for SCARNA12 Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA12 Gene

No ASD Table

Relevant External Links for SCARNA12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCARNA12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCARNA12 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCARNA12 Gene:


SOURCE GeneReport for Unigene cluster for SCARNA12 Gene:

genes like me logo Genes that share expression patterns with SCARNA12: 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 SCARNA12 Gene

Orthologs for SCARNA12 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SCARNA12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia snoU89 35
  • 99 (a)
(Canis familiaris)
Mammalia snoU89 35
  • 80 (a)
(Mus musculus)
Mammalia Gm23547 35
  • 72 (a)
(Bos Taurus)
Mammalia snoU89 35 35 35
  • 69 (a)
(Monodelphis domestica)
Mammalia snoU89 35
  • 65 (a)
Species where no ortholog for SCARNA12 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • zebrafish (Danio rerio)

Evolution for SCARNA12 Gene

Gene Tree for SCARNA12 (if available)
Gene Tree for SCARNA12 (if available)

Paralogs for SCARNA12 Gene

No data available for Paralogs for SCARNA12 Gene

Variants for SCARNA12 Gene

Sequence variations from dbSNP and Humsavar for SCARNA12 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1005764929 -- 6,968,678(+) TATGC(C/T)CTGTG intron-variant, upstream-variant-2KB
rs1006174159 -- 6,967,281(+) GCAGG(A/T)CTCAA intron-variant, nc-transcript-variant, downstream-variant-500B
rs1007038736 -- 6,969,402(+) AAGAG(A/G)CCTAA intron-variant, upstream-variant-2KB
rs1007787763 -- 6,968,199(+) CAAGA(C/T)TTGGC intron-variant, upstream-variant-2KB
rs1009095157 -- 6,969,198(+) TATAG(G/T)AAGTC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SCARNA12 Gene

Variant ID Type Subtype PubMed ID
nsv1035811 CNV gain 25217958
nsv1047373 CNV gain 25217958
nsv509453 CNV insertion 20534489

Relevant External Links for SCARNA12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SCARNA12 Gene

Disorders for SCARNA12 Gene

Relevant External Links for SCARNA12

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SCARNA12 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCARNA12 Gene

Publications for SCARNA12 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) 3 64
  2. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination. (PMID: 9074930) Ansari-Lari M.A. … Gibbs R.A. (Genome Res. 1997) 3 64
  3. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13. (PMID: 8723724) Ansari-Lari M.A. … Gibbs R.A. (Genome Res. 1996) 3 64

Products for SCARNA12 Gene

Sources for SCARNA12 Gene

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