Table I All experimentally observed alternative translation initiation sites (aTIS: 1231 human, 465 mouse) were mapped onto their corresponding reference genomes (Ensembl human GRCh37 and mouse NCBIM37). The dTIS locations were detected throughout several mass spectrometry analyses and a compilation was extracted from the in-house ms-lims system (109) obtained from previously generated N-terminal proteomics data ((50, 5557) and previously unpublished data) (supplemental Table S1). The overlap with annotated Ensembl, Swiss-Prot or TrEMBL annotated TIS is also provided. For the Ensembl mapping an extra subdivision was done based on TIS location in the first (Exon1) or the consecutive exons (Exon>1). Also, a comparison was made with the TIS identified within two ribosome profiling studies on HEK293 and mESC cell lines (18,19). See the “selection of N-termini” paragraph within the material and methods section for more explanation on the subdivision based on confidence level (either H or L). “(+ meta)” indicates that available isoform, transcript, Ribo-seq and/or orthologues dTIS metadata is available for dTIS originally assigned as low confidence (See also supplemental Table S1)
Human dTISMouse dTIS
Confidence levelTotalConfidence levelTotal
HLHL
Identified peptides8583731231274191465
Mapped peptides8503701220
Ensembl TIS
    Exon14144525429
    Exon>11463217839342
    Subtotal1873622364771
No Ensembl TIS
    Exon13014734812848176
    Exon>136228764982136218
    Subtotal663334997210184394
Swiss-Prot isoform TIS1711836137
No Swiss-Prot isoform TIS8333691202238190428
TrEMBL TIS1593219143649
No TrEMBL TIS6913381029213185416
Ribo-seq TIS969105571269
No Ribo-seq TIS7543611115217179396
Identified peptides(+meta)9003311231298167465
Mapped peptides(+meta)8923281220