The GTF annotation and the analysis of HIV-1 splice-site conservation do not include the A4d splice acceptor. However, A4d is used by NL4-3 and appears to be less conserved across HIV-1 strains (https://journals.asm.org/doi/10.1128/jvi.02515-16?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed).