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Aliases for SCARNA2 Gene
Subcategory (RNA class) for SCARNA2 Gene
snoRNA
Aliases for SCARNA2 Gene
- Small Cajal Body-Specific RNA 2 (HGNC, NCBI Entrez Gene, Ensembl)
- MgU2-25/61 (HGNC, NCBI Entrez Gene)
- HBII-382 (HGNC, NCBI Entrez Gene)
- SCARNA2 (Ensembl, snOPY)
- NONHSAG002325.2 (NONCODE)
- Lnc-TMEM167B-1 (LNCipedia)
- HSALNG0005856 (LncBook)
- SNODB1614 (snoDB)
- RF01268 (Rfam)
External Ids for SCARNA2 Gene
- HGNC: 32558
- NCBI Entrez Gene: 677766
- Ensembl: ENSG00000278249
Previous GeneCards Identifiers for SCARNA2 Gene
- GC01P109444
- GC01P109642
- GC01P107536
- GC01P109101
- GC01P109105
- GC01P109114
- GC01P109116
- GC01P109110
- GC01P109108
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
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 | 250.7 | +0.6 | 558 | 2.5 | ZSCAN16 CHD2 TBP ZBTB10 SP1 MXD4 CEBPA NR2C1 MNT DEK | ENSG00000270066 RF01268 SCARNA2 ENSG00000258634 PRPF38B RPL17P7 STRIP1 ENSG00000228665 SLC25A24 GPR61 | |
| GH01J109095 | Enhancer | 0.8 | Ensembl ENCODE | 0.7 | -4.0 | -3954 | 1.3 | ZNF217 REST CTBP1 ZNF316 ZBTB40 SMARCE1 FOXA1 PKNOX1 MAFG MAFF | C1orf194 ENSG00000270066 NDUFB3P1 SCARNA2 TMEM167B NONHSAG002324.2 ELAPOR1 | |
| GH01J109094 | Enhancer | 0.8 | Ensembl ENCODE | 0.4 | -5.5 | -5486 | 1 | ZNF2 ZFP37 ZNF24 ZBTB48 SCRT1 SP7 ZNF366 KLF10 ZXDB ZEB2 | NDUFB3P1 C1orf194 NONHSAG002324.2 TMEM167B ENSG00000270066 SCARNA2 ELAPOR1 | |
| GH01J109093 | Enhancer | 0.2 | Ensembl | 0.4 | -6.4 | -6391 | 0.4 | NDUFB3P1 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
Latest Assembly
- chr1:109,100,192-109,100,612
- (GRCh38/hg38)
- Size:
- 421 bases
- Orientation:
- Plus strand
Previous Assembly
- chr1:109,642,815-109,643,234
- (GRCh37/hg19 by Entrez Gene)
- Size:
- 420 bases
- Orientation:
- Plus strand
Genomic View for SCARNA2 Gene
Genes around SCARNA2 on UCSC Golden Path with GeneCards custom track
SCARNA2 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path
- Cytogenetic band:
-
- 1q13.1 by HGNC
- 1p13.3 by Entrez Gene
- 1p13.3 by Ensembl
SCARNA2 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for SCARNA2 Gene
Proteins for SCARNA2 Gene
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
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
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SCARNA2 - Starting at $85 >
- * SCARNA2 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
Inhibitory RNAs for research
Clone products for research
- Applied Biological Materials (abm): Clones for SCARNA2 - Starting at $45 >
- * SCARNA2 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
Cell Lines for research
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
| Compartment | Confidence |
|---|---|
| mitochondrion | 1 |
| nucleus | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005730 | nucleolus | IEA | -- |
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
No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for SCARNA2 Gene
Transcripts for SCARNA2 Gene
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 | 421 | 7 |
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 | 3917 | 2 |
LNCipedia: lnc-TMEM167B-1:1, NONCODE: NONHSAT005013.2, |
| URS0000EB4911_9606 | lncRNA | 612 | 1 |
LncBook: HSALNT0012178, |
| URS0000D576B2_9606 | lncRNA | 421 | 1 |
LNCipedia: lnc-TMEM167B-1:5, |
| URS0000D5CBEB_9606 | lncRNA | 415 | 1 |
LNCipedia: lnc-TMEM167B-1:4, |
SCARNA2 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path
Additional transcripts not in RNAcentral for SCARNA2 Gene
- 1 NCBI additional mRNA sequence :
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SCARNA2 - Starting at $85 >
- * SCARNA2 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
Inhibitory RNAs for research
Clone products for research
- Applied Biological Materials (abm): Clones for SCARNA2 - Starting at $45 >
- * SCARNA2 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
Relevant External Links for SCARNA2 Gene
- GeneLoc Exon Structure for
- SCARNA2
Expression for SCARNA2 Gene
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCARNA2
SOURCE GeneReport for Unigene cluster for SCARNA2 Gene:
Hs.550815Gene Expression Assays for research
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
No data available for Orthologs for SCARNA2 Gene
Paralogs for SCARNA2 Gene
No data available for Paralogs for SCARNA2 Gene
Variants for SCARNA2 Gene
All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).
| 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
SNP Genotyping and Copy Number Assays for research
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
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| dubowitz syndrome |
|
|
Search SCARNA2 in MalaCards
View complete list of genes associated with diseases
Additional Disease Information for SCARNA2
No data available for UniProtKB/Swiss-Prot and Genatlas for SCARNA2 Gene
Publications for SCARNA2 Gene
- 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
- 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
- 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
- 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
- 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
Products for SCARNA2 Gene
- Browse OriGene Antibodies
- Custom Antibody Services
- Browse OriGene ELISA Kits
- Custom Assay Services
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for SCARNA2
- Origene Custom Protein Services for SCARNA2
- Browse OriGene Inhibitory RNA Products For SCARNA2
- Browse OriGene qPCR primer pairs and template standards
- Browse CRISPR knockouts for SCARNA2
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Browse OriGene miRNA Products For SCARNA2
- Browse Sino Biological cDNA Clones
- Browse Sino Biological Recombinant Proteins
- Browse Sino Biological Cell Lysates
- Browse Sino Biological Antibodies
- Browse Sino Biological Assays
- Browse ELISA Kits
- Browse CRO Services
- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for knockout CRISPR/Cas9 clones, lentivirus, and/or AAV products for SCARNA2
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles, and/or promoter clone products for SCARNA2
- Search GeneCopoeia for miRNA 3'UTR Target clone products for SCARNA2
- Search GeneCopoeia for shRNA, lentivirus, and/or AAV clone products for SCARNA2
Sources for SCARNA2 Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM® (Updated: 05-Mar-2021)
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) MedlinePlus Genetics
- (111) MeSH
- (112) MedlinePlus
- (113) CDC
- (114) NINDS
- (115) NCBI Bookshelf
- (116) ClinVar
- (117) Gene Damage Index
- (118) HPO
- (119) UDN
- (120) VISTA
- (121) FANTOM5
- (122) ENCODE
- (123) ProSci
- (124) Horizon
- (125) The Signaling Pathways Project (SPP)
- (126) IID
- (127) VectorBuilder
- (128) SNPedia
- (129) BRCA Exchange
- (130) CIViC
- (131) ProteoGenix
- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNAcentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Open Targets Platform
- (175) 5SRRNADB
- (176) snoDB
- (177) MirGeneDB