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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 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
GH12F006923 1.5 FANTOM5 ENCODE 30.4 +40.5 40456 6.8 HDGF ARID4B SIN3A ZNF2 YY1 ZNF143 FOS DEK PAF1 ZNF263 LRRC23 SCARNA12 ENSG00000219410 ENSG00000247853 RPL13P5 USP5 PHB2 EMG1 SPSB2 NOP2
GH12F006940 1.6 FANTOM5 ENCODE 21.7 +13.9 13948 25.9 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SPSB2 ENSG00000219410 ENSG00000247853 NOP2 NCAPD2 SCARNA12 ENSG00000256967 LOC100419825 LOC100420983 DPPA3
GH12F006762 1.6 FANTOM5 ENCODE 19.2 +201.2 201202 7.2 HDGF PKNOX1 ARNT MLX CREB3L1 ZFP64 ARID4B SIN3A FEZF1 ZNF2 ENSG00000219410 ENSG00000247853 NCAPD2 SPSB2 NOP2 ENSG00000256967 C1RL-AS1 GDF3 SCARNA12 TNFRSF1A
GH12F006546 1.5 FANTOM5 ENCODE 18.4 +415.7 415691 10.3 HDGF PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ENSG00000219410 ENSG00000247853 NCAPD2 TAPBPL PHB2 NOP2 SCARNA12 VAMP1 SPSB2 SCARNA11
GH12F006880 0.9 ENCODE 29.4 +86.7 86735 1.6 ZFP64 ARID4B DMAP1 ZSCAN9 ZNF354C ZNF138 ZNF202 ZNF680 ZNF654 ZBTB11 ENSG00000219410 SPSB2 ENSG00000247853 C12orf57 SCARNA12 GNB3 NOP2 C1RL-AS1 PHB2 NCAPD2
- 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

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

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 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 and mRNA Expression by UniProt/SwissProt 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
rs111506788 -- 6,968,235(+) CGAGT(C/G)CTATC intron-variant, upstream-variant-2KB
rs111666132 -- 6,967,052(+) CAGAG(A/T)AGCCA intron-variant, downstream-variant-500B
rs112269622 -- 6,967,383(+) CTACC(A/G/T)TGGAC intron-variant, nc-transcript-variant
rs112401532 -- 6,967,675(+) GGATA(G/T)CATCT intron-variant, upstream-variant-2KB, splice-donor-variant
rs113285640 -- 6,967,170(+) ACTCA(C/G/T)CGTCT downstream-variant-500B, splice-donor-variant

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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