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    NOVA2 NOVA alternative splicing regulator 2 [ Homo sapiens (human) ]

    Gene ID: 4858, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NOVA2provided by HGNC
    Official Full Name
    NOVA alternative splicing regulator 2provided by HGNC
    Primary source
    HGNC:HGNC:7887
    See related
    Ensembl:ENSG00000104967 MIM:601991; AllianceGenome:HGNC:7887
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ANOVA; NOVA3; NEDASB; NOVA-2
    Summary
    Enables sequence-specific mRNA binding activity. Involved in neuron differentiation and regulation of alternative mRNA splicing, via spliceosome. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 7.5), fat (RPKM 2.1) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NOVA2 in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45933734..45973865, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (48761166..48801293, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46436992..46477123, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14829 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10804 Neighboring gene Myb related transcription factor, partner of profilin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10805 Neighboring gene nanos C2HC-type zinc finger 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46430224-46430724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14831 Neighboring gene CRISPR/Cas9-targeted silencer 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46455793-46456740 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr19:46463595-46464168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14833 Neighboring gene Sharpr-MPRA regulatory region 4903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46506355-46506854 Neighboring gene coiled-coil domain containing 61 Neighboring gene Sharpr-MPRA regulatory region 13926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10808 Neighboring gene microRNA 769

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Alternative Splicing Changes Promoted by NOVA2 Upregulation in Endothelial Cells and Relevance for Gastric Cancer. Di Matteo A, et al. Int J Mol Sci, 2023 Apr 30. PMID 37175811, Free PMC Article
    2. ANOVA, a putative astrocytic RNA-binding protein gene that maps to chromosome 19q13.3. Ueki K, et al. Neurogenetics, 1997 May. PMID 10735272
    3. De novo truncating NOVA2 variants affect alternative splicing and lead to heterogeneous neurodevelopmental phenotypes. Scala M, et al. Hum Mutat, 2022 Sep. PMID 35607920, Free PMC Article
    4. Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Lewis HA, et al. Cell, 2000 Feb 4. PMID 10676814
    5. MiR-7-5p suppresses tumor metastasis of non-small cell lung cancer by targeting NOVA2. Xiao H. Cell Mol Biol Lett, 2019. PMID 31832068, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circ_0004140 promotes lung adenocarcinoma progression by upregulating NOVA2 via sponging miR-330-5p.
      Title: Circ_0004140 promotes lung adenocarcinoma progression by upregulating NOVA2 via sponging miR-330-5p.
    2. Circ_0102231 inactivates the PI3K/AKT signaling pathway by regulating the miR-635/NOVA2 pathway to promote the progression of non-small cell lung cancer.
      Title: Circ_0102231 inactivates the PI3K/AKT signaling pathway by regulating the miR-635/NOVA2 pathway to promote the progression of non-small cell lung cancer.
    3. METTL14 reverses liver fibrosis by inhibiting NOVA2 through an m6A-YTHDF2-dependent mechanism.
      Title: METTL14 reverses liver fibrosis by inhibiting NOVA2 through an m6A-YTHDF2-dependent mechanism.
    4. Alternative Splicing Changes Promoted by NOVA2 Upregulation in Endothelial Cells and Relevance for Gastric Cancer.
      Title: Alternative Splicing Changes Promoted by NOVA2 Upregulation in Endothelial Cells and Relevance for Gastric Cancer.
    5. Neuro-oncological Ventral Antigen 2 Regulates Splicing of Vascular Endothelial Growth Factor Receptor 1 and Is Required for Endothelial Function.
      Title: Neuro-oncological Ventral Antigen 2 Regulates Splicing of Vascular Endothelial Growth Factor Receptor 1 and Is Required for Endothelial Function.
    6. Circ_0016760 Serves as a Cancer Promoter in Non-small Cell Lung Cancer Through miR-876-3p/NOVA2 Axis.
      Title: Circ_0016760 Serves as a Cancer Promoter in Non-small Cell Lung Cancer Through miR-876-3p/NOVA2 Axis.
    7. De novo truncating NOVA2 variants affect alternative splicing and lead to heterogeneous neurodevelopmental phenotypes.
      Title: De novo truncating NOVA2 variants affect alternative splicing and lead to heterogeneous neurodevelopmental phenotypes.
    8. PART1 destabilized by NOVA2 regulates blood-brain barrier permeability in endothelial cells via STAU1-mediated mRNA degradation.
      Title: PART1 destabilized by NOVA2 regulates blood-brain barrier permeability in endothelial cells via STAU1-mediated mRNA degradation.
    9. MiR-7-5p suppresses tumor metastasis of non-small cell lung cancer by targeting NOVA2.
      Title: MiR-7-5p suppresses tumor metastasis of non-small cell lung cancer by targeting NOVA2.
    10. The NOVA2 variant protein shows decreased ability to bind target RNA sequences.
      Title: De Novo Frameshift Variants in the Neuronal Splicing Factor NOVA2 Result in a Common C-Terminal Extension and Cause a Severe Form of Neurodevelopmental Disorder.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
    MedGen: C5394311 OMIM: 618859 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables sequence-specific mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in central nervous system neuron development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of RNA metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of alternative mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding protein Nova-2
    Names
    astrocytic NOVA1-like RNA-binding protein
    neuro-oncological ventral antigen 2
    neuro-oncological ventral antigen 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_002516.4 → NP_002507.1  RNA-binding protein Nova-2

      See identical proteins and their annotated locations for NP_002507.1

      Status: REVIEWED

      Source sequence(s)
      AC008623, AC011545, AF083898, AI990298, BM666426, BQ631784, U70477
      Consensus CDS
      CCDS12679.1
      UniProtKB/Swiss-Prot
      O43267, Q9UEA1, Q9UNW9
      Related
      ENSP00000263257.4, ENST00000263257.6
      Conserved Domains (3) summary
      cd09031
      Location:409 → 477
      KH-I_NOVA_rpt3; third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova)
      cd22435
      Location:33 → 104
      KH-I_NOVA_rpt1; first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova)
      cd22436
      Location:131 → 200
      KH-I_NOVA_rpt2; second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      45933734..45973865 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006723230.4 → XP_006723293.1  RNA-binding protein Nova-2 isoform X1

      See identical proteins and their annotated locations for XP_006723293.1

      Conserved Domains (2) summary
      cd09031
      Location:300 → 368
      KH-I_NOVA_rpt3; third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova)
      cd22436
      Location:22 → 91
      KH-I_NOVA_rpt2; second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      48761166..48801293 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321106.1 → XP_054177081.1  RNA-binding protein Nova-2 isoform X1

    2. XM_054321107.1 → XP_054177082.1  RNA-binding protein Nova-2 isoform X1

    3. XM_054321105.1 → XP_054177080.1  RNA-binding protein Nova-2 isoform X1

    4. XM_054321108.1 → XP_054177083.1  RNA-binding protein Nova-2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UNW9.1 GenPept UniProtKB/Swiss-Prot:Q9UNW9

    Gene LinkOut

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