Overview of Bioinformatic Analysis for Functional Predictions. The diagram shows an overview of the bioinformatic analyses performed in order to make functional predictions about the genes of interest based on (a) the predicted amino acid sequence, b predicted protein structure, and (c) genomic comparisons with selected species. The bioinformatic tool used for each type of analysis is indicated. Multiple approaches were used in order to obtain informational results for each gene of interest and to increase confidence in the overall predictions

Homology model of P1 putative kinase domain. The kinase domain of Receptor-interacting serine/threonine-protein kinase 2 (RIPK2, 6fu5.1.B in the rcsb protein database) is the template used for the homology modelling of P1. The X-RAY diffraction 3.26 Å was used to determine the experimental structure of 6fu5.1 [60]. The blue color show regions of the model where P1 was well-modeled and orange regions where P1 was poorly modeled. The well-modeled regions (blue) are regions where P1 is likely to be similar to the experimental 3D structure of the template. The homology model pertains to the putative kinase domain of P1 and starts from P1 residue N°3 (GLN, Glutamine) and ends with the residue N° 284 (LYS, Lysine)

Homology model of P3. T cell receptor beta chain (3of6.1.A in the rcsb protein database) is the template used for the homology modelling of P3. The homology model starts from the P3 residue N°32 (THR, Threonine) and ends with the residue N° 245 (THR, Threonine). The X-RAY diffraction 2.80 Å was used to determine the experimental structure of 3of6.1.A [61]. The blue color show regions of the model in which P3 was well-modeled by the template, and orange regions where P3 was poorly modeled. The blue regions correspond to the T cell receptor beta chain immunoglobulin domains

Homology model of P10 chemokine interleukin-8-like domain. Lymphotactin (1j8i.1.A in the rcsb protein database) is the template used for the homology modelling of P10. The homology model starts from P10 residue N°24 (GLU, Glutamic acid) and ends with the residue N° 102 (SER, Serine). The NMR spectroscopy was used to determine the experimental structure of 1j8i.1.A [62]. The blue color show regions of the model where P10 was well modeled and orange regions where P10 was poorly modeled. The chemokine interleukin-8-like domain of the model starts with P10 amino acid at position N°27(HIS, Histidine) and ends with amino acid at position N°86 ((LEU, Leucine). This region includes both well-modeled (blue) and poorly-modeled (orange) sections

Homology model of P11. Maltase-glucoamylase, intestinal (3top.1.A in the rcsb protein database) is the template used for the homology modelling of P11. The X-RAY diffraction 2.9 Å was used to determine the experimental structure of 3top.1.A [63]. The homology model starts from P11 residue N°922 (LYS, Lysine) and ends with the residue N° 1804 (PHE, Phenylalanine). The P-type trefoil domain (amino acid N°51–962), galactose mutaros domain (amino acid N°114–1085), and glycoside hydrolase domain (amino acid N°225–1152) are not covered in the homology model. The blue color show regions of the model where P11 was well modeled and orange regions show where P11 was poorly modeled

Expression level of selected zebrafish genes in other published studies. Expression level of selected zebrafish genes (P1, P9, and P12) in other published RNA-seq datasets of (a) zebrafish heart regeneration [64], and (b) zebrafish brain microglia [52] using the Zf Regeneration Database (www.zfregeneration.org, [65]). The y-axis indicates the normalized transcript level expressed as fpkm (fragments per kilobase of exon per million reads). On the x-axis is the different experimental conditions. (A,  dpa =  days post injury. B, active microglia indicates responding to acute damage, h = hours after acute damage)