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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SCARNA4 Gene

RNA gene   GIFtS: 20
GCID: GC01M155895

Small Cajal Body-Specific RNA 4

  Search for SCARNA4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Subcategory (RNA class): scaRNA

Quality score for this RNA gene is 11

Aliases
Small Cajal Body-Specific RNA 41 2
ACA262

External Ids:    HGNC: 325601   Entrez Gene: 6777712   Ensembl: ENSG000002528087   
ORGUL members:    fRNAdb10:FR059316 FR059316      
H-InvDB12:HIT000383029 HIT000383029    
NCBI13:AL355388 AJ609483    
NONCODE14:u3347      
Rfam:RF00423    
RNAdb15:SNO1202    

Export aliases for SCARNA4 gene to outside databases

Previous GC identifers: GC01M154162 GC01M127256


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for SCARNA4 Gene: 
SCARNA4 (small Cajal body-specific RNA 4) is an RNA gene, and is affiliated with the scaRNA class.

fRNAdb sequence ontologies for SCARNA4 - the ORGUL cluster for this gene includes several descriptions:
Small Cajal body specific RNA 15 - scaRNAs are a specific class of small nuclear RNAs which localise to the Cajal bodies and guide the modification of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA45 belongs to the H/ACA box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail structure, the conserved H/ACA-box motifs and is found associated with GAR1 [2]. ACA45 is predicted to guide the pseudouridylation of residue U37 of the U2 spliceosomal snRNA [2].
snoRNA - A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.

View fRNAdb secondary structures for SCARNA4

(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  NT_004487.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SCARNA4 gene promoter:
         NF-1/L   NF-1   POU3F1   AP-4   CUTL1   CREB   AREB6   deltaCREB   Pax-4a   ATF6   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCARNA4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q22   Ensembl cytogenetic band:  1q22   HGNC cytogenetic band: 1q22

SCARNA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCARNA4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M155895:  view genomic region     (about GC identifiers)

Start:
155,895,749 bp from pter      End:
155,895,877 bp from pter
Size:
129 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SCARNA4

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
SCARNA: ncRNAs / Small nucleolar RNAs : Small cajal body-specific

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCARNA4

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
1 fRNAdb Secondary structure:


Unigene Cluster for SCARNA4:

Small Cajal body-specific RNA 4
Hs.678903
Unigene Representative Sequence: BF814437
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000516999(snoRNA)
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Additional mRNA sequence: AJ609483.1 

1 DOTS entry:

DT.97838465 

GeneLoc Exon Structure


(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 SCARNA4:H-invDB

SCARNA4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SCARNA4 Expression
About this image


SOURCE GeneReport for Unigene cluster: Hs.678903
    SABiosciences Custom PCR Arrays for SCARNA4
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In Situ
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(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

This gene was present in the common ancestor of mammals.

Orthologs for SCARNA4 gene from 1/2 species (see all 2)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
oppossum
(Monodelphis domestica)
Mammalia SCARNA46
SCARNA46
Small Cajal body specific RNA 4
83(a)
61(a)
many → 1
possible ortholog
2(190775389-190775517)
1(112938987-112939119)


ENSEMBL Gene Tree for SCARNA4 (if available)
TreeFam Gene Tree for SCARNA4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

4 SNPs in SCARNA4 are shown    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs343427551,2
C--155896130(+) TTTTTT/-TTTTT 1 -- us2k11Minor allele frequency- -:0.50NA 2
rs723786261,2
----155897595(+) TCTCC-/AAAAAA 1 -- us2k10--------
rs3687918121,2
----155897704(+) CCTCT-/CTTAAGG 1 -- us2k10--------
rs3720165191,2
----155896116(+) TGGCA-/TTTTTTT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for SCARNA4 (155895749 - 155895877 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SCARNA4:    About this table     
Variant IDTypeSubtypePubMed ID
esv33869CNV Loss17666407

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SCARNA4 for disorders           About MalaCards
OMIM information: 115665 116600 121800 155600 211420 600975 605225 605606 606788 606852 606928 607317 607671 608446 608543 608553 608995    

SCARNA4 for disorders           About GeneDecksing


Export disorders for SCARNA4 gene to outside databases

(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

PubMed articles for SCARNA4 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SCARNA4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A common sequence motif determines the Cajal body-spec ific localization of box H/ACA scaRNAs. (PubMed id 12912925)1 Richard P....Kiss T. (2003)
  2. 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)
  3. (PubMed id 2431280)10 
  4. (PubMed id 15103394)10 
  5. (PubMed id 15199136)10 
  6. (PubMed id 165188)10 
  7. (PubMed id 16381836)10 
  8. (PubMed id 15608158)10 
  9. (PubMed id 18089548)10 
  10. (PubMed id 15608161)10 

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 677771 HGNC: 32560 Ensembl:ENSG00000252808 euGenes: HUgn677771 ECgene: SCARNA4
H-InvDB: SCARNA4

(According to HUGE)
About This Section
  --

(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
NameDescription
PharmGKB entry for SCARNA4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SCARNA4 gene:
Search GeneIP for patents involving SCARNA4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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
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