Free for academic non-profit institutions. Other users need a Commercial license

SCARNA4 Gene(RNA Gene)

Small Cajal Body-Specific RNA 4

GCID:
GC01M155925
GIFtS:
17
Genes Participants
UDN Logo

Aliases for SCARNA4 Gene

Subcategory (RNA class) for SCARNA4 Gene

scaRNA

Quality Score for this RNA gene is

12

Aliases for SCARNA4 Gene

  • Small Cajal Body-Specific RNA 4 2 3 5
  • ACA26 ScaRNA 3
  • ACA26 3

External Ids for SCARNA4 Gene

ORGUL Members for SCARNA4 Gene

Previous GeneCards Identifiers for SCARNA4 Gene

  • GC01M154162
  • GC01M155895
  • GC01M127256

Summaries for SCARNA4 Gene

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 Gene - the ORGUL cluster for this gene includes several descriptions:

  • 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.

  • 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].

Additional gene information for SCARNA4 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for SCARNA4 Gene

Genomics for SCARNA4 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for SCARNA4 Gene

Promoters and enhancers for SCARNA4 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
GH01I155965 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12 -49.3 -49291 19 MLX ZFP64 FEZF1 DMAP1 IRF4 SLC30A9 ZNF213 ZNF416 ZNF143 ZNF263 ARHGEF2 RIT1 KHDC4 GON4L CLK2 PAQR6 PRCC RRNAD1 YY1AP1 ENSG00000271267
GH01I156000 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.6 -76.4 -76392 3.6 FOXA2 ARID4B ZNF121 ZNF263 SMARCB1 ZNF592 MAFF SMARCA4 STAT3 HMBOX1 LOC105371729 RIT1 RXFP4 KHDC4 LAMTOR2 UBQLN4 SCARNA4 MEX3A LMNA SNORA80E
GH01I155958 Enhancer 1.2 Ensembl ENCODE dbSUPER 12.1 -35.0 -35043 4.4 NFIB INSM2 KLF17 SIN3A RAD21 POLR2B RCOR1 FOS IKZF2 RUNX3 RIT1 LOC107985210 ARHGEF2 KHDC4 SCARNA4 LAMTOR2 UBQLN4 LOC107985209 MIR6738
GH01I156004 Enhancer 0.7 ENCODE dbSUPER 11.6 -79.2 -79158 1.2 ELF3 SAP130 SP5 EGR2 ARHGEF2 RXFP4 KHDC4 UBQLN4 LAMTOR2 SCARNA4 RIT1 MEX3A LMNA SNORA80E
GH01I155949 Enhancer 0.6 dbSUPER 12.4 -25.5 -25549 3.6 MEIS2 PKNOX1 EBF1 GABPA RELA ZNF121 GABPB1 SPI1 MIR6738 RIT1 SCARNA4 LOC107985210 ARHGEF2 SNORA80E UBQLN4 LAMTOR2 LMNA MEX3A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCARNA4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCARNA4 gene promoter:

Genomic Locations for SCARNA4 Gene

Genomic Locations for SCARNA4 Gene
chr1:155,925,958-155,926,086
(GRCh38/hg38)
Size:
129 bases
Orientation:
Minus strand
chr1:155,895,749-155,895,877
(GRCh37/hg19)

Genomic View for SCARNA4 Gene

Genes around SCARNA4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARNA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARNA4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SCARNA4 Gene

ORGUL Member Location for SCARNA4 Gene

ORGUL Member Location for SCARNA4 gene

Proteins for SCARNA4 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

Post-translational modifications for SCARNA4 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SCARNA4 Gene

Domains & Families for SCARNA4 Gene

Gene Families for SCARNA4 Gene

HGNC:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCARNA4: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SCARNA4 Gene

Function for SCARNA4 Gene

Products:

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

Phenotypes From GWAS Catalog for SCARNA4 Gene

Animal Model Products

Clone 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 SCARNA4 Gene

Localization for SCARNA4 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for SCARNA4 Gene

Pathways & Interactions for SCARNA4 Gene

SuperPathways for SCARNA4 Gene

PathCards logo More details on SuperPathways for SCARNA4
No Data Available

Interacting Proteins for SCARNA4 Gene

Gene Ontology (GO) - Biological Process for SCARNA4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SCARNA4 Gene

Drugs & Compounds for SCARNA4 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SCARNA4 Gene

Products:

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

mRNA/cDNA for SCARNA4 Gene

(1) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SCARNA4 Gene

Small Cajal body-specific RNA 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARNA4 Gene

No ASD Table

Relevant External Links for SCARNA4 Gene

GeneLoc Exon Structure for
SCARNA4
ECgene alternative splicing isoforms for
SCARNA4

Expression for SCARNA4 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCARNA4 Gene

mRNA expression in normal human tissues for SCARNA4 Gene
mRNA expression by GTEx for SCARNA4 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCARNA4 Gene:

SCARNA4

SOURCE GeneReport for Unigene cluster for SCARNA4 Gene:

Hs.678903
genes like me logo Genes that share expression patterns with SCARNA4: 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 SCARNA4 Gene

Orthologs for SCARNA4 Gene

Evolution for SCARNA4 Gene

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

No data available for Orthologs for SCARNA4 Gene

Paralogs for SCARNA4 Gene

No data available for Paralogs for SCARNA4 Gene

Variants for SCARNA4 Gene

Sequence variations from dbSNP and Humsavar for SCARNA4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1001258993 -- 155,927,807(-) A/G upstream_transcript_variant
rs1001697220 -- 155,926,295(-) T/C upstream_transcript_variant
rs1007870728 -- 155,927,097(-) T/C upstream_transcript_variant
rs1009887704 -- 155,927,565(-) G/A upstream_transcript_variant
rs1010048756 -- 155,926,274(-) T/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SCARNA4 Gene

Variant ID Type Subtype PubMed ID
esv33869 CNV loss 17666407

Additional Variant Information for SCARNA4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARNA4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SCARNA4 Gene

Disorders for SCARNA4 Gene

Additional Disease Information for SCARNA4

ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SCARNA4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCARNA4 Gene

Publications for SCARNA4 Gene

  1. Human box H/ACA pseudouridylation guide RNA machinery. (PMID: 15199136) Kiss AM … Kiss T (Molecular and cellular biology 2004) 1 3 58
  2. Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs. (PMID: 12032087) Darzacq X … Kiss T (The EMBO journal 2002) 1 3 58
  3. A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs. (PMID: 12912925) Richard P … Kiss T (The EMBO journal 2003) 3 58
  4. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. (PMID: 18089548) Genome Information Integration Project And H-Invitational 2 … Gojobori T (Nucleic acids research 2008) 1
  5. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. (PMID: 16381836) Lestrade L … Weber MJ (Nucleic acids research 2006) 1

Products for SCARNA4 Gene

Sources for SCARNA4 Gene

Content
Loading form....