SCARNA12 Gene
RNA gene GIFtS: 17
GCID: GC12M007076
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small Cajal body-specific RNA 12
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Aliases
for SCARNA12 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
Subcategory (RNA class): scaRNA
Quality score for this RNA gene is 3
| Aliases |
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| Small Cajal Body-Specific RNA 121 2 | | U891 2 |
| External Ids: | HGNC: 325691 | Entrez Gene: 6777772 | Ensembl: ENSG000002387957 |
Export aliases for SCARNA12 gene to outside databasesPrevious GC identifer: GC12M006947
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Summaries
for SCARNA12 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for SCARNA12:
This gene produces a small nuclear RNA that localizes specifically to Cajal bodies, which are conserved subnuclearorganelles that are present in the nucleoplasm. This RNA is processed from an intron of the prohibitin 2 host gene. Itincludes both an H/ACA box and a C/D box, and is thought to guide the pseudouridylation of residue U46 in the U5 smallnuclear RNA. (provided by RefSeq, Jun 2010)
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Genomic Views
for SCARNA12 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000012.11 NC_018923.1 NT_009759.16
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the SCARNA12 gene promoter:
SRF Sp1 SRF (504 AA) HFH-1 ATF-2 MyoD c-Jun MRF-2 c-Myc
Other transcription factors
Search SABiosciences Chromatin IP Primers for SCARNA12
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCARNA12 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 12p13.31 Ensembl cytogenetic band: 12p13.31 HGNC cytogenetic band: 12p13.31SCARNA12 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 12 GeneLoc Exon Structure GeneLoc location for GC12M007076: view genomic region
(about GC identifiers)
Start:
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7,076,500 bp from pter |
End:
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7,076,769 bp from pter |
Size:
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270 bases |
Orientation:
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minus strand |
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Proteins
for SCARNA12 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
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UniProtKB: --
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Protein
Domains /
Families
for SCARNA12 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| -- |
Function
for SCARNA12 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
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Pathways & Interactions
for SCARNA12 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
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Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCARNA12
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Drugs & Compounds
for SCARNA12 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for SCARNA12
Search CenterWatch for drugs/clinical trials and news about SCARNA12 
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Transcripts
for SCARNA12 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
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Unigene Cluster for SCARNA12: Small Cajal body-specific RNA 12 Hs.689636 Unigene Representative Sequence: AY0777391 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000459155(snoRNA)
Additional cDNA sequence: AY077739.1
GeneLoc Exon Structure
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Expression
for SCARNA12 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| Expression evidence for SCARNA12:none
SCARNA12 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ACTCCCCACT
About this image
SOURCE GeneReport for Unigene cluster: Hs.689636
SABiosciences Custom PCR Arrays for SCARNA12
Primer
Products: |  | Browse OriGene genome-wide validated SYBR primer pairs
Browse OriGene validated miRNA SYBR primer pairs
| | | Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat SCARNA12 | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCARNA12 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SCARNA12 |
Orthologs
for SCARNA12 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
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ENSEMBL Gene Tree for SCARNA12 (if available)
TreeFam Gene Tree for SCARNA12 (if available) |
Paralogs
for SCARNA12 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
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Genomic Variants
for SCARNA12 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
| | SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for SCARNA12 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
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Publications
for SCARNA12 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
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PubMed articles for SCARNA12 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SCARNA12) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs. (PubMed id 12032087)1 Darzacq X....Kiss T. (2002)
- Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination. (PubMed id 9074930)1 Ansari-Lari M.A....Gibbs R.A. (1997)
- A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13. (PubMed id 8723724)1 Ansari-Lari M.A....Gibbs R.A. (1996)
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External Searches for SCARNA12 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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Genome Databases showing SCARNA12 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
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Other Databases showing SCARNA12 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing SCARNA12 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for SCARNA12 | Pharmacogenomics, SNPs, Pathways |
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About This Section
| Patent Information for SCARNA12 gene:
Search GeneIP for patents involving SCARNA12
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Products
for SCARNA12 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
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|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat SCARNA12 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SCARNA12 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCARNA12 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SCARNA12 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SCARNA12 | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCARNA12 |
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 | | | | |  |  |  | | | | Search ThermoFisher Antibodies for SCARNA12 |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SCARNA12 |
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Last full update: 18 Mar 2013 -
Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013
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