Deubiquitinase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins (PubMed:29626158, PubMed:30951545). May therefore play an important regulatory role at the level of protein turnover by preventing degradation of proteins through the removal of conjugated ubiquitin (PubMed:29626158, PubMed:30951545). Specifically hydrolyzes 'Lys-63'-, 'Lys-48'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitins chains (By similarity). Essential component of TGF-beta/BMP signaling cascade (By similarity). Specifically deubiquitinates monoubiquitinated SMAD4, opposing the activity of E3 ubiquitin-protein ligase TRIM33 (By similarity). Deubiquitinates alkylation repair enzyme ALKBH3 (By similarity). OTUD4 recruits USP7 and USP9X to stabilize ALKBH3, thereby promoting the repair of alkylated DNA lesions (By similarity). Deubiquitinates mTORC2 complex component RICTOR at 'Lys-294' by removing 'Lys-63'-linked polyubiquitin chains, stabilizing RICTOR and enhancing its binding to MTOR, thus promoting mTORC2 complex assembly (By similarity). Regulates chromosome alignment and segregation in mitosis by regulating the localization of BIRC5/survivin to mitotic centromeres (By similarity). Involved in axonal growth and neuronal cell migration (PubMed:24607389). Regulates cellular clock function by enhancing the protein stability and transcriptional activity of the core circadian protein ARNTL/BMAL1 via its deubiquitinating activity (PubMed:29626158). Deubiquitinates PEG10 (PubMed:30951545). Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Interacts with SMAD4, MARK4, NUAK1 and BIRC5/survivin. Interacts with DCX. Interacts with OTUD4 and USP7; the interaction is direct (By similarity). Interacts with ARNTL/BMAL1 (PubMed:29626158). Interacts with RICTOR; the interaction results in deubiquitination of RICTOR and protection from proteasomal degradation (By similarity). Highest levels in liver and brain with expression also detected in heart, muscle, spleen and kidney (at protein leve) (PubMed:33378666). Ubiquitously expressed in adult tissues (PubMed:9178254). At least expressed from 17 dpc to 21 postnatal days. Brain-specific USP9X deletion results in early postnatal death, whereas forebrain-specific deletion is compatible with survival to adulthood. In the absence of USP9X the cortical architecture is disorganized, and neurons display reduced neurite growth. Belongs to the peptidase C19 family.