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Additional file 1: Fig. S1 The Tceal7 gene is derived from the domestication of L1 retrotransposon fragments. Fig. S2 The Bex/Tceal gene cluster was established before the diversification of extant eutherians. Fig. S3 Highly diverged BEX/TCEAL proteins share a coiled coil domain. Fig. S4 BEX/TCEAL proteins might have inherited some of their structural properties from the ancestral transposon. Fig. S5 Selection pressure analyses reveal signatures of positive selection in the Bex/Tceal genes. Fig. S6 A BGW-like sequence was already present in the GLA promoter of the last therian common ancestor. Fig. S7 Bex/Tceal genes show tissue-enriched expression patterns during development. Fig. S8 Bex3 and Tceal7 genes, but not the ancestral HALEX element, induce cell proliferation in chicken neural tube. Fig. S9 The deletions introduced using CRISPR-Cas9 technology can be observed in the mRNA expressed from the Bex3 mutant alleles. Fig. S10 CRISPR-Cas9-generated Bex3 mutant alleles show subtle skull abnormalities. Fig. S11 Bex3 mutant mice show normal acoustic startle reflex. Fig. S12 Bex3 deficiency leads to aberrant mTOR signaling in the brain. Table S1 Coding genes putatively derived from transposable elements in the human and mouse genomes. Table S2 Altered expression of BEX and TCEAL genes in subjects with autism spectrum disorder or schizophrenia. Table S3 Enrichment of differential gene expression in BEX and TCEAL gene families in subjects with autism spectrum disorder or schizophrenia. Table S4 Primers and reconstructed gene sequences used in this work. Supplementary references.

Additional file 2. Review history.

Additional Figure 1. Protein-coding gene AUPR plots. Metric prediction performance computed on promoter and transcript sequences for annotate protein-coding homologs (AUPR on y-axis and n, the number of consecutive nucleotides in n-gram metrics, on x-axis). (PDF 158 kb)

Additional file 5: Table S1. List of oligonucleotides used for qPCR experiments.

Additional Figure 2. NONCODE ROC curves. ROC curves computed on promoter and transcript sequences for NONCODE lncRNA homologs (for n-gram metrics, n=12 has been chosen). (PDF 822 kb)

Additional Figure 3. ZFLNC ROC curves. ROC curves computed on promoter and transcript sequences for ZFLNC lncRNA homologs (for n-gram metrics, n=12 has been chosen). (PDF 1580 kb)

Additional file 1: Figure S1. Control MO-Fluo in 72 hpf S. purpuratus embryos. Sea urchin embryos at 72 hpf from oral (a, b, c), lateral (a′, b′, c′) and vegetal (a″, b″, c″) views depict the tissues where fluorescence deriving from the fluorescent MO is visible (c–c″). Morphant embryos imaged with microscope (b–b″) present a phenotype similar to uninjected control embryos (a–a″).

Figure S3. Prediction performance in terms of AUPR for different feature selection algorithms at increasing size of the signature in zebrafish. (PDF 72 kb)

Figure S1. Prediction performance in terms of AUPR for different feature selection algorithms at increasing size of the signature in human. (PDF 72 kb)

Figure S2. Prediction performance in terms of AUPR for different feature selection algorithms at increasing size of the signature in mouse. (PDF 72 kb)

Table S3. Clusters of highly correlated features. (PDF 31 kb)

Figure S4. Hierarchical clusters of top 20 features selected by different algorithms computed with Jaccard distance, i.e. ratio between intersection and union of two sets, and complete linkage.(PDF 37 kb)

Figure S4. Hierarchical clusters of top 20 features selected by different algorithms computed with Jaccard distance, i.e. ratio between intersection and union of two sets, and complete linkage.(PDF 37 kb)

Figure S3. Prediction performance in terms of AUPR for different feature selection algorithms at increasing size of the signature in zebrafish. (PDF 72 kb)

Figure S1. Prediction performance in terms of AUPR for different feature selection algorithms at increasing size of the signature in human. (PDF 72 kb)

Figure S2. Prediction performance in terms of AUPR for different feature selection algorithms at increasing size of the signature in mouse. (PDF 72 kb)

Table S3. Clusters of highly correlated features. (PDF 31 kb)

Intron conservation. This survey inferred the existence of a conserved intron code in Rab32 and Rab38 subfamily retained after a vertebrate duplication. Switch I (partial) and Switch II domains are underlined. (DOCX 15 kb)

Additional syntenic studies. A. Human chromosome 11 and mouse chromosome 7: a focus on Rab38 gene loci with, respectively, a TRIM gene family expansion and an extraordinary clustering of olfactory genes: Vomeronasal 2 receptor (Vmn2r) and Olfactory Receptor (OR) in mouse; B Microsynteny of Rab32LO between echinoderms and cephalochordates. (PPTX 72.8 kb)

Phylogenies of Tab, Nox, Fzd, Stxbp. (PDF 378 kb)

Gene expression profile during amphioxus development. Rab32/38 and Rab32LO gene expression profiles by real time RT-PCR during Branchiostoma lanceolatum development. Both genes have been normalized using the ribosomal protein L32 (RPL32) expression using the same cDNA template. (DOCX 41.4 kb)

Vertebrate Rab32 and Rab38 phylogeny. (PDF 178 kb)

GRM phylogeny. (PDF 282 kb)