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SCARNA4 Gene

RNA gene GIFtS: 17
GCID: GC01M155895

Small Cajal Body-Specific RNA 4

Search for SCARNA4
at

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:

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:

DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB: --

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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Interactions:

Search GeneGlobe Interaction Network for SCARNA4

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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1 fRNAdb Secondary structure:

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000516999(snoRNA)

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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™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for SCARNA4:H-invDB

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

SCARNA4 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

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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)
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--

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)
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(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs34342755^1,2	C	--	155896130(+)	`TTTTTT/-TTTTT`	1	--	us2k¹		1		NA	2
rs72378626^1,2	--	--	155897595(+)	`TCTCC-/AAAAAA`	1	--	us2k¹		0	--	--	--	--
rs368791812^1,2	--	--	155897704(+)	`CCTCT-/CTTAAGG`	1	--	us2k¹		0	--	--	--	--
rs372016519^1,2	--	--	155896116(+)	`TGGCA-/TTTTTTT`	1	--	us2k¹		0	--	--	--	--

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

Structural Variations
Database of Genomic Variants (DGV) 1 variation for SCARNA4: About this table

Variant ID	Type	Subtype	PubMed ID
esv33869	CNV	Loss	17666407

Site Specific Mutation Identification with PCR Assays

Search QIAGEN SeqTarget long-range PCR primers for resequencing SCARNA4

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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.)
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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)
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PubMed articles for SCARNA4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SCARNA4)

Utopia: connect your pdf to the dynamic
world of online information

A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs. (PubMed id 12912925)¹ Richard P....Kiss T. (EMBO J. 2003)
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. (EMBO J. 2002)
(PubMed id 2431280)¹⁰
(PubMed id 15103394)¹⁰
(PubMed id 15199136)¹⁰
(PubMed id 165188)¹⁰
(PubMed id 16381836)¹⁰
(PubMed id 15608158)¹⁰
(PubMed id 18089548)¹⁰
(PubMed id 15608161)¹⁰

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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)
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Entrez Gene: 677771	HGNC: 32560	Ensembl:ENSG00000252808	euGenes: HUgn677771	ECgene: SCARNA4
H-InvDB: SCARNA4

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for SCARNA4	Pharmacogenomics, SNPs, Pathways

Intellectual Property for SCARNA4 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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Small Cajal Body-Specific RNA 4

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SCARNA4 Gene

Small Cajal Body-Specific RNA 4

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