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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
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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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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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