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Table 2 Functional annotation of retained genes into broad functional categories, assembled transcripts can be retrieved via

From: Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens

Pp transcript (putative retained gene) taxonomic group homolog broad functional category (potential) functional category details
PPP_2925_C1 bacteria Membrane-bound lytic murein transglycosylase B cytotoxicity murein degradation murein-degrading enzyme, may play a role in recycling of muropeptides during cell
BJ203770 bacteria putative protease cytotoxicity protease  
PPP_4234_C1 metazoa cytolysin I cytotoxicity cytotoxicity involved in pore-formation
PPP_3510_C1 cyano RTX toxins and related Ca2+-binding proteins cytotoxicity cytotoxicity  
PPP_1172_C1 bacteria Enoyl-CoA hydratase/carnithine racemase metabolism fatty acid metabolism  
PPP_6629_C1 bacteria mannosylglycerate synthase metabolism sugar metabolism  
PPP_5746_C1 metazoa L-kynurenine 3-monooxygenase Fpk metabolism amino acid metabolism  
PPP_8479_C1 metazoa COMMD2 metabolism copper metabolism COMM (copper metabolism MURR1) domain containing 2
BJ173412 metazoa ubiquitin metabolism protein metabolism ribosomal protein in C. elegans dehydrogenases
PPP_3987_C1 fungi MNN9 metabolism N-glycosylation  
PPP_6514_C1 cyano oxidoreductase metabolism energy metabolism related to aryl-alcohol dehydrogenases
PPP_11394_C1 bacteria homolog of eukaryotic DNA ligase III nucleic acid binding / modification DNA repair  
BJ191550 bacteria formamidopyrimidine-DNA glycosylase nucleic acid binding / modification DNA repair  
BJ160862 metazoa Osa1 nuclear protein nucleic acid binding / modification DNA binding chromatin regulation
BJ582496 cyano SAM-dependent methyltransferase nucleic acid binding / modification nucleic acid modification  
PPP_2586_C1 bacteria CarD protein signal transduction DNA binding leucine zipper transcription factor, light- and starvation-induced response
PPP_3689_C1 bacteria serine/threonine protein kinase signal transduction signal transduction  
BJ172132 bacteria serine/threonine protein kinase signal transduction signal transduction  
PPP_460_C1 metazoa HLA-B-associated transcript signal transduction signal transduction  
PPP_1041_C1 metazoa calcium/calmodulin-dependent protein kinase II delta signal transduction signal transduction  
PPP_6326_C1 metazoa tumor suppressor tout-velu signal transduction signal transduction involved in diffusion of hedgehog
PPP_11399_C1 metazoa dual-specificity tyrosine phosphatase YVH1 signal transduction signal transduction Non-receptor class dual specificity subfamily
PPP_184_C1 fungi high-affinity iron permease transport transport high affinity iron uptake
PPP_7115_C2 fungi uric acid-xanthine permease transport transport belongs to the Xanthine/Uracil oermeases family
PPP_11191_C1 fungi inorganic phosphate transporter transport transport probable inorganic phosphate transporter; yeast pho99 homologue