New Genomic Signals Underlying the Emergence of Human Proto-Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Datasets
2.2. Intron Search
2.3. Motif Search
2.4. UTR Analyses
2.5. Domain Annotation
2.6. Statistical and Bioinformatic Analyses
3. Results
3.1. Introns
3.1.1. Introns in Proto-Genes
3.1.2. Origin of Introns in “Intergenic” Proto-Genes
3.2. Motifs Upstream Proto-Genes
3.2.1. Average Number of Motifs from “MotifsAllUpstream”
3.2.2. Distribution of “MotifsCore” Motifs
3.3. UTRs of Proto-Genes
3.3.1. Size and GC Content of UTRs
3.3.2. 2D Structure of the 5′ UTRs
3.4. Domains in Proto-Genes
3.4.1. Annotated Domains
3.4.2. Novel Domains in Proto-Proteins
4. Discussion
4.1. Introns
4.2. Motifs
4.3. UTRs
4.4. Domains
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
5′ UTRs | 5′ Untranslated regions |
lncRNA | long non-coding RNA |
UCSC | University of California Santa Cruz |
bp | base pairs |
TSS | transcription starting site |
PSSM | position-specific scoring matrix |
MFE | minimum free energy |
GO | Gene Ontology |
RPM | Million Mapped reads |
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Age Class | Genomic Position | Mean Proportion of Proto-Genes with Intron |
---|---|---|
I0 | “exonic” | 71.4 |
I1 | “exonic” | 97.4 |
I2 | “exonic” | 84 |
I3 | “exonic” | 89.5 |
I4 | “exonic” | 90.7 |
I5 | “exonic” | 98 |
I0 | “intronic” | 11.6 |
I1 | “intronic” | 24.25 |
I2 | “intronic” | 32.4 |
I3 | “intronic” | 31.9 |
I4 | “intronic” | 33.95 |
I5 | “intronic” | 32.2 |
I0 | “intergenic” | 3.2 |
I1 | “intergenic” | 5.5 |
I2 | “intergenic” | 5.23 |
I3 | “intergenic” | 6.22 |
I4 | “intergenic” | 8.8 |
I5 | “intergenic” | 30.8 |
Age Class | Genomic Position 1 | Genomic Position 2 | p-Value t Test |
---|---|---|---|
I0 | “exonic” | “intronic” | 5.602 × 10−7 |
I0 | “exonic” | “intergenic” | 5.362 × 10−8 |
I0 | “intronic” | “intergenic” | 2.2 × 10−16 |
I1 | “exonic” | “intronic” | 1.972 × 10−5 |
I1 | “exonic” | “intergenic” | 6.549 × 10−7 |
I1 | “intronic” | “intergenic” | 1.469 × 10−15 |
I2 | “exonic” | “intronic” | 2.928 × 10−5 |
I2 | “exonic” | “intergenic” | 1.269 × 10−8 |
I2 | “intronic” | “intergenic” | 2.2 × 10−16 |
I3 | “exonic” | “intronic” | 1.995 × 10−9 |
I3 | “exonic” | “intergenic” | 2.2 × 10−16 |
I3 | “intronic” | “intergenic” | 2.2 × 10−16 |
I4 | “exonic” | “intronic” | 2.2 × 10−16 |
I4 | “exonic” | “intergenic” | 2.2 × 10−16 |
I4 | “intronic” | “intergenic” | 2.2 × 10−16 |
I5 | “exonic” | “intronic” | 2.2 × 10−16 |
I5 | “exonic” | “intergenic” | 2.2 × 10−16 |
I5 | “intronic” | “intergenic” | 7.034 × 10−7 |
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Grandchamp, A.; Berk, K.; Dohmen, E.; Bornberg-Bauer, E. New Genomic Signals Underlying the Emergence of Human Proto-Genes. Genes 2022, 13, 284. https://doi.org/10.3390/genes13020284
Grandchamp A, Berk K, Dohmen E, Bornberg-Bauer E. New Genomic Signals Underlying the Emergence of Human Proto-Genes. Genes. 2022; 13(2):284. https://doi.org/10.3390/genes13020284
Chicago/Turabian StyleGrandchamp, Anna, Katrin Berk, Elias Dohmen, and Erich Bornberg-Bauer. 2022. "New Genomic Signals Underlying the Emergence of Human Proto-Genes" Genes 13, no. 2: 284. https://doi.org/10.3390/genes13020284
APA StyleGrandchamp, A., Berk, K., Dohmen, E., & Bornberg-Bauer, E. (2022). New Genomic Signals Underlying the Emergence of Human Proto-Genes. Genes, 13(2), 284. https://doi.org/10.3390/genes13020284