Key component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. In the SEC complex, AFF4 acts as a central scaffold that recruits other factors through direct interactions with ELL proteins (ELL, ELL2 or ELL3) and the P-TEFb complex. In case of infection by HIV-1 virus, the SEC complex is recruited by the viral Tat protein to stimulate viral gene expression (By similarity). Component of the super elongation complex (SEC), at least composed of EAF1, EAF2, CDK9, MLLT3/AF9, AFF (AFF1 or AFF4), the P-TEFb complex and ELL (ELL, ELL2 or ELL3). Interacts with ELL2; the interaction is direct and leads to stabilize ELL2 and prevent ELL2 ubiquitination and degradation (By similarity). Interacts with ELL3; the interaction is direct. Associates to transcriptionally active chromatin but not at snRNA genes. Highly expressed in testis by Sertoli cells, and at low levels in other tissues. Expressed throughout embryogenesis with maximum expression at 10.5 and 12.5 dpc. Mice are infertile with azoospermia. Spermatogenesis is arrested at the level of spermiogenesis. Belongs to the AF4 family.