SCARNA2 Gene (RNA Gene)

Small Cajal Body-Specific RNA 2

GC01P109108
GIFtS:
16
See more...

Aliases for SCARNA2 Gene

Subcategory (RNA class) for SCARNA2 Gene

snoRNA

Number of RNA Genes sources:

6 / 17

Aliases for SCARNA2 Gene

  • Small Cajal Body-Specific RNA 2 2 3 5
  • SCARNA2 2 5 170
  • MgU2-25/61 2 3
  • HBII-382 2 3
  • NONHSAG002325.2 91
  • Lnc-TMEM167B-1 165
  • SNODB1614 177
  • RF01268 168

External Ids for SCARNA2 Gene

Previous GeneCards Identifiers for SCARNA2 Gene

  • GC01P109444
  • GC01P109642
  • GC01P107536
  • GC01P109101
  • GC01P109105
  • GC01P109114
  • GC01P109116
  • GC01P109110

Summaries for SCARNA2 Gene

GeneCards Summary for SCARNA2 Gene

SCARNA2 (Small Cajal Body-Specific RNA 2) is an RNA Gene, and is affiliated with the snoRNA class. Diseases associated with SCARNA2 include Dubowitz Syndrome.

Rfam classification for SCARNA2 Gene

  • Small Cajal body-specific RNA 2

Additional gene information for SCARNA2 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for SCARNA2 Gene

Genomics for SCARNA2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SCARNA2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J109099 Promoter/Enhancer 1.9 Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.5 508 2.6 ZNF221 ARHGAP35 SP1 HNRNPL CREB1 GATAD2A CTCF ZNF629 PRDM10 REST ENSG00000270066 SCARNA2 ENSG00000258634 PRPF38B ENSG00000244716 C1orf194 ENSG00000228665 STRIP1 SLC25A24 GSTM2
GH01J109098 Enhancer 0.2 Ensembl 600.7 -1.4 -1392 0.4 ENSG00000270066 SCARNA2 C1orf194 NDUFB3P1 TMEM167B ELAPOR1
GH01J109095 Enhancer 0.8 Ensembl ENCODE 0.7 -4.1 -4055 1.5 PRDM10 FOXA1 REST SOX6 SCRT2 ZNF766 ESR1 CTBP1 ZNF444 ZNF316 C1orf194 ENSG00000270066 NDUFB3P1 SCARNA2 NONHSAG002324.2 TMEM167B ELAPOR1
GH01J109104 Promoter/Enhancer 0.6 Ensembl dbSUPER 0.7 +4.2 4208 0.4 POLR2A ENSG00000251484 LOC100420092 MN308770 ENSG00000270066 SCARNA2 ELAPOR1 TMEM167B
GH01J109094 Enhancer 0.8 Ensembl ENCODE 0.4 -5.5 -5455 0.9 PRDM10 ZNF629 ZNF692 ZNF600 SCRT2 ZNF10 ZXDB CEBPB BCL11A ZBTB48 NDUFB3P1 C1orf194 NONHSAG002324.2 TMEM167B ENSG00000270066 SCARNA2 ELAPOR1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCARNA2 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the SCARNA2 gene promoter:
  • C/EBPbeta
  • COUP
  • COUP-TF
  • COUP-TF1
  • E2F
  • E2F-1
  • HNF-4alpha1
  • HNF-4alpha2
  • SRY
  • TBP

Genomic Locations for SCARNA2 Gene

Genomic Locations for SCARNA2 Gene
chr1:109,100,193-109,100,612
(GRCh38/hg38)
Size:
420 bases
Orientation:
Plus strand
chr1:109,642,815-109,643,241
(GRCh37/hg19)
Size:
427 bases
Orientation:
Plus strand

Genomic View for SCARNA2 Gene

Genes around SCARNA2 on UCSC Golden Path with GeneCards custom track
SCARNA2 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
SCARNA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SCARNA2 Gene

Proteins for SCARNA2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

Post-translational modifications for SCARNA2 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA2 Gene

Domains & Families for SCARNA2 Gene

Gene Families for SCARNA2 Gene

HGNC:
genes like me logo Genes that share domains with SCARNA2: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SCARNA2 Gene

Function for SCARNA2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Animal Model Products

CRISPR Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SCARNA2 Gene

Localization for SCARNA2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCARNA2 gene
Compartment Confidence
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SCARNA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with SCARNA2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for SCARNA2 Gene

Pathways & Interactions for SCARNA2 Gene

PathCards logo

SuperPathways for SCARNA2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCARNA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SCARNA2: view

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for SCARNA2 Gene

Drugs & Compounds for SCARNA2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SCARNA2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

Non-coding RNA (ncRNA) Transcripts from RNAcentral for SCARNA2 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000023DE4C_9606 snoRNA 420 8

HGNC: 32558,

RefSeq: NR_003023,

Ensembl: ENST00000458748 (view in UCSC) ,

LNCipedia: lnc-TMEM167B-1:3,

Rfam: RF01268,

snoDB: SNODB1614,

snOPY: Homo_sapiens300776,

ENA: BK005568.1:1..420:ncRNA,

URS00008B3922_9606 lncRNA 3916 2

LNCipedia: lnc-TMEM167B-1:1,

NONCODE: NONHSAT005013.2,

URS0000D576B2_9606 lncRNA 421 1

LNCipedia: lnc-TMEM167B-1:5,

URS0000D5CBEB_9606 lncRNA 414 1

LNCipedia: lnc-TMEM167B-1:4,

SCARNA2 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for SCARNA2 Gene

1 NCBI additional mRNA sequence :

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA2 Gene

No ASD Table

Relevant External Links for SCARNA2 Gene

GeneLoc Exon Structure for
SCARNA2

Expression for SCARNA2 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCARNA2 Gene

mRNA expression in normal human tissues for SCARNA2 Gene
mRNA expression by GTEx for SCARNA2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCARNA2

SOURCE GeneReport for Unigene cluster for SCARNA2 Gene:

Hs.550815
genes like me logo Genes that share expression patterns with SCARNA2: 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 SCARNA2 Gene

Orthologs for SCARNA2 Gene

Evolution for SCARNA2 Gene

ENSEMBL:
Gene Tree for SCARNA2 (if available)
TreeFam:
Gene Tree for SCARNA2 (if available)

No data available for Orthologs for SCARNA2 Gene

Paralogs for SCARNA2 Gene

No data available for Paralogs for SCARNA2 Gene

Variants for SCARNA2 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Additional dbSNP identifiers (rs#s) for SCARNA2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SCARNA2 Gene

Variant ID Type Subtype PubMed ID
esv3894001 CNV gain 25118596
nsv1008458 CNV gain 25217958
nsv831026 CNV loss 17160897

Additional Variant Information for SCARNA2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for SCARNA2 Gene

Disorders for SCARNA2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCARNA2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
dubowitz syndrome
  • dubowitz's syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCARNA2

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCARNA2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCARNA2 Gene

Publications for SCARNA2 Gene

  1. Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa. (PMID: 15556860) Tycowski KT … Steitz JA (Current biology : CB 2004) 2 3
  2. The lncRNA SCARNA2 mediates colorectal cancer chemoresistance through a conserved microRNA-342-3p target sequence. (PMID: 30443961) Zhang PF … Zhang XM (Journal of cellular physiology 2019) 3
  3. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3
  4. The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region. (PMID: 19906720) Gérard MA … Carbon P (Nucleic acids research 2010) 3
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3

ExternalLinks

View latest publications for SCARNA2 gene in Mastermind

Products for SCARNA2 Gene

Sources for SCARNA2 Gene