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Aliases for NOVA2 Gene

Aliases for NOVA2 Gene

  • NOVA Alternative Splicing Regulator 2 2 3 5
  • Neuro-Oncological Ventral Antigen 2 2 3 4
  • Astrocytic NOVA1-Like RNA-Binding Protein 3 4
  • Neuro-Oncological Ventral Antigen 3 2 3
  • NOVA3 3 4
  • ANOVA 3 4
  • RNA-Binding Protein Nova-2 3

External Ids for NOVA2 Gene

Previous HGNC Symbols for NOVA2 Gene

  • NOVA3

Previous GeneCards Identifiers for NOVA2 Gene

  • GC19M047086
  • GC19M046833
  • GC19M051118
  • GC19M051134
  • GC19M046442
  • GC19M042871

Summaries for NOVA2 Gene

GeneCards Summary for NOVA2 Gene

NOVA2 (NOVA Alternative Splicing Regulator 2) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is NOVA1.

UniProtKB/Swiss-Prot for NOVA2 Gene

  • May regulate RNA splicing or metabolism in a specific subset of developing neurons (By similarity). Binds single strand RNA.

Additional gene information for NOVA2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NOVA2 Gene

Genomics for NOVA2 Gene

Regulatory Elements for NOVA2 Gene

Enhancers for NOVA2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H046263 1 ENCODE 20 -289.6 -289553 0.2 FEZF1 ELK1 FOS ATF7 RUNX3 SP3 YY2 JUNB TSHZ1 ZNF585B ZC3H4 IRF2BP1 CCDC61 PPP5D1 ENSG00000269124 NOVA2 ENSG00000268810 PNMA8A HIF3A IGFL4
GH19H046782 1.4 ENCODE dbSUPER 10.5 -812.2 -812236 6.8 MLX FEZF1 DMAP1 ZNF143 SP3 NFYC ZFP41 MEF2D SSRP1 ZNF610 ZC3H4 CCDC61 BICRA PRKD2 CCDC9 NOP53-AS1 SLC1A5 ENSG00000268810 SYMPK SNORD23
GH19H046600 1.4 ENCODE dbSUPER 9.8 -628.8 -628849 4.6 DMAP1 YY1 ZNF143 SP3 ZC3H11A NFYC ZNF610 GLIS1 RCOR2 NBN ZC3H4 ENSG00000268810 CCDC61 ENSG00000269148 CCDC9 FBXO46 IRF2BP1 INAFM1 PPP5D1 PNMA8A
GH19H045250 1.3 FANTOM5 ENCODE 9.8 +721.4 721412 2.9 HDGF YBX1 GLIS2 ZNF143 KLF7 SP3 ZNF592 ZNF610 SMARCA4 ZNF184 ZNF235 MARK4 MRPS15P2 ZNF180 ZNF285 IRF2BP1 ZNF112 ERCC2 ENSG00000267114 RELB
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NOVA2 on UCSC Golden Path with GeneCards custom track

Promoters for NOVA2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000110296 46 1001 MXI1 SP3 KLF1 ATF1 ZSCAN4 ZNF398 SP1 ZFHX2 GLIS2 CTBP1

Genomic Locations for NOVA2 Gene

Genomic Locations for NOVA2 Gene
39,813 bases
Minus strand

Genomic View for NOVA2 Gene

Genes around NOVA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NOVA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NOVA2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NOVA2 Gene

Proteins for NOVA2 Gene

  • Protein details for NOVA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RNA-binding protein Nova-2
    Protein Accession:
    Secondary Accessions:
    • O43267
    • Q9UEA1

    Protein attributes for NOVA2 Gene

    492 amino acids
    Molecular mass:
    49009 Da
    Quaternary structure:
    • Interacts with PTBP2; the interaction is direct.
    • Sequence=AAB88661.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NOVA2 Gene

neXtProt entry for NOVA2 Gene

Post-translational modifications for NOVA2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NOVA2 Gene

No data available for DME Specific Peptides for NOVA2 Gene

Domains & Families for NOVA2 Gene

Gene Families for NOVA2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NOVA2 Gene

Suggested Antigen Peptide Sequences for NOVA2 Gene

Graphical View of Domain Structure for InterPro Entry



  • The third KH domain (KH3) recognizes specifically 5-UCAY-3.
  • The third KH domain (KH3) recognizes specifically 5-UCAY-3.
genes like me logo Genes that share domains with NOVA2: view

Function for NOVA2 Gene

Molecular function for NOVA2 Gene

GENATLAS Biochemistry:
neuro-oncological ventral antigen 2
UniProtKB/Swiss-Prot Function:
May regulate RNA splicing or metabolism in a specific subset of developing neurons (By similarity). Binds single strand RNA.

Phenotypes From GWAS Catalog for NOVA2 Gene

Gene Ontology (GO) - Molecular Function for NOVA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,NAS 10735272
genes like me logo Genes that share ontologies with NOVA2: view

Phenotypes for NOVA2 Gene

genes like me logo Genes that share phenotypes with NOVA2: view

Animal Models for NOVA2 Gene

MGI Knock Outs for NOVA2:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NOVA2 Gene

Localization for NOVA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NOVA2 Gene

Subcellular locations from

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 NOVA2 gene
Compartment Confidence
nucleus 4
cytosol 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NOVA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with NOVA2: view

Pathways & Interactions for NOVA2 Gene

SuperPathways for NOVA2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NOVA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IEA --
GO:0051252 regulation of RNA metabolic process IEA --
genes like me logo Genes that share ontologies with NOVA2: view

No data available for Pathways by source and SIGNOR curated interactions for NOVA2 Gene

Drugs & Compounds for NOVA2 Gene

No Compound Related Data Available

Transcripts for NOVA2 Gene

Unigene Clusters for NOVA2 Gene

Neuro-oncological ventral antigen 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NOVA2 Gene

No ASD Table

Relevant External Links for NOVA2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NOVA2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NOVA2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NOVA2 Gene

This gene is overexpressed in Brain - Cortex (x4.3).

Protein differential expression in normal tissues from HIPED for NOVA2 Gene

This gene is overexpressed in Fetal Brain (17.5), Pancreas (10.0), Fetal gut (7.7), Plasma (7.6), and Peripheral blood mononuclear cells (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NOVA2 Gene

Protein tissue co-expression partners for NOVA2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NOVA2 Gene:


SOURCE GeneReport for Unigene cluster for NOVA2 Gene:


mRNA Expression by UniProt/SwissProt for NOVA2 Gene:

Tissue specificity: Brain. Expression restricted to astrocytes.

Evidence on tissue expression from TISSUES for NOVA2 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with NOVA2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NOVA2 Gene

Orthologs for NOVA2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NOVA2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NOVA2 34
  • 100 (a)
(Bos Taurus)
Mammalia NOVA2 33 34
  • 93.56 (n)
(Canis familiaris)
Mammalia NOVA2 34
  • 93 (a)
(Mus musculus)
Mammalia Nova2 33 16 34
  • 90.99 (n)
(Rattus norvegicus)
Mammalia Nova2 33
  • 89.05 (n)
(Monodelphis domestica)
Mammalia NOVA2 34
  • 89 (a)
(Gallus gallus)
Aves -- 34
  • 24 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nova2 33
  • 68.1 (n)
(Danio rerio)
Actinopterygii nova1 34
  • 77 (a)
Dr.6502 33
fruit fly
(Drosophila melanogaster)
Insecta ps 35 34
  • 50 (a)
(Caenorhabditis elegans)
Secernentea Y59A8B.10 34
  • 24 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PBP2 34
  • 22 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 43 (a)
Species where no ortholog for NOVA2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NOVA2 Gene

Gene Tree for NOVA2 (if available)
Gene Tree for NOVA2 (if available)

Paralogs for NOVA2 Gene

Paralogs for NOVA2 Gene

(1) SIMAP similar genes for NOVA2 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with NOVA2: view

Variants for NOVA2 Gene

Sequence variations from dbSNP and Humsavar for NOVA2 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs1000299650 -- 45,969,859(+) TCACA(-/G)TGCCC intron-variant
rs1000346128 -- 45,933,808(+) TGTGG(G/T)GGGGG utr-variant-3-prime
rs1000348891 -- 45,939,795(+) GTTGG(A/C/G)GGGGA utr-variant-3-prime
rs1000401402 -- 45,940,685(+) ACGGG(A/G)CCTGC reference, synonymous-codon
rs1000482032 -- 45,964,161(+) TTTCT(C/T)TTTTT intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for NOVA2 Gene

Variant ID Type Subtype PubMed ID
esv2674835 CNV deletion 23128226
esv3644515 CNV loss 21293372
nsv1071540 CNV deletion 25765185
nsv1114017 CNV deletion 24896259
nsv1143918 CNV deletion 24896259
nsv953588 CNV deletion 24416366

Variation tolerance for NOVA2 Gene

Residual Variation Intolerance Score: 28.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.24; 5.36% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NOVA2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NOVA2 Gene

Disorders for NOVA2 Gene

Relevant External Links for NOVA2

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for NOVA2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NOVA2 Gene

Publications for NOVA2 Gene

  1. Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains. (PMID: 10368286) Lewis HA … Burley SK (Structure (London, England : 1993) 1999) 2 3 4 60
  2. The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia. (PMID: 9789075) Yang YY … Darnell RB (Proceedings of the National Academy of Sciences of the United States of America 1998) 3 4 22 60
  3. ANOVA, a putative astrocytic RNA-binding protein gene that maps to chromosome 19q13.3. (PMID: 10735272) Ueki K … Louis DN (Neurogenetics 1997) 3 4 22 60
  4. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 60
  5. Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. (PMID: 10676814) Lewis HA … Burley SK (Cell 2000) 3 4 60

Products for NOVA2 Gene

Sources for NOVA2 Gene

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