Functions to regulate alternative splicing in neurons by binding pre-mRNA in a sequence-specific manner to activate exon inclusion or exclusion (PubMed:8558240, PubMed:15933722, PubMed:17065982, PubMed:14615540). It binds specifically to the sequences 5'-YCAY-3' and regulates splicing in only a subset of regulated exons (PubMed:9154818, PubMed:8558240, PubMed:14615540). Binding to an exonic 5'-YCAY-3' cluster changes the protein complexes assembled on pre-mRNA, blocking U1 snRNP binding and exon inclusion, whereas binding to an intronic 5'-YCAY-3' cluster enhances spliceosome assembly and exon inclusion (PubMed:10719891). Binding to 5'-YCAY-3' clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons. Binding to an exonic 5'-YCAY-3' cluster changed the protein complexes assembled on pre-mRNA, blocking U1 snRNP (small nuclear ribonucleoprotein) binding and exon inclusion, whereas binding to an intronic 5'-YCAY-3' cluster enhanced spliceosome assembly and exon inclusion (PubMed:17065982, PubMed:15933722). With NOVA1, they perform unique biological functions in different brain areas and cell types (PubMed:30638744). Autoregulates its own expression by acting as a splicing repressor (PubMed:15933722). Acts to activate the inclusion of exon E3A in the glycine receptor alpha-2 chain and of exon E9 in gamma-aminobutyric-acid receptor gamma-2 subunit via a distal downstream UCAU-rich intronic splicing enhancer (PubMed:12808107). Acts to regulate a novel glycine receptor alpha-2 chain splice variant (alpha-2N) in developing spinal cord (PubMed:17065982). Interacts with PTBP2; the interaction is direct. Expressed in neurons of the cortex, sub-cortex, cerebellum and brainstem (at protein level)(PubMed:10829067). Expressed in motor neurons, but not in glia (PubMed:10829067). The KH domain consists of approximately 70 amino acids and includes a conserved hydrophobic core, an invariant Gly-X-X-Gly motif, and an additional variable segment. The third KH domain (KH3) binds a hairpin RNA loop containing the 5'-UCAY-3' motif on targeted molecules. RNA binding by KH3 requires residues C-terminal to the KH domain. Defects in Nova1 leads to neuronal death in spinal and brainstem neurons.