Gene Structure Evolution of the Short-Chain Dehydrogenase/Reductase (SDR) Family
Abstract
:1. Introduction
2. Methods
3. Results and Discussion
3.1. Gene Structure of Vertebrate and Invertebrate Variants of SDR Families
3.2. Gene Structure of Human SDR7C and SDR42E Family Variants
3.3. Invertebrate Orthologs of Human SDR Family Variants
3.4. Human SDR7C4 and SDR42E1 Are Possibly Active Retrogenes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Family Symbol and Name | Enzyme Symbol | Gene Symbol | Gene ID | Chr | Exon Number | Phase Formula | aa n. | Structure Consensus | Catalysis Consensus |
---|---|---|---|---|---|---|---|---|---|
SDR7C1 | RDH11 | 51109 | 14 | 7 | 122221 | 318 | GANTGIG | YCHSK | |
SDR7C2 | RDH12 | 145226 | 316 | ||||||
SDR7C | SDR7C3 | RDH13 | 112724 | 19 | 7 | 122222 | 331 | ||
SDR7C4 | RDH14 | 57665 | 12 | 2 | 0 | 336 | GANSGLG | YSRSK | |
Retinol dehydrogenase | SDR7C5 | DHRS13 | 147015 | 17 | 5 | 2022 | 377 | GANSGIG | YADTK |
SDR40C Dehydrogenase/reductase SDR family | SDR40C1 | DHRS12 | 79758 | 13 | 10 | 120020022 | 317 | GGNSGIG | YAQNK |
% Identity | |||||
---|---|---|---|---|---|
SDR7C1 | SDR7C2 | SDR7C3 | SDR7C4 | SDR7C5 | |
SDR7C2 | 71.66 | ||||
SDR7C3 | 49.68 | 48.87 | |||
SDR7C4 | 46.15 | 46.47 | 48.88 | ||
SDR7C5 | 45.78 | 46.41 | 42.32 | 44.48 | |
SDR40C1 | 32.54 | 33.22 | 30.64 | 31.21 | 28.23 |
Species | Variants | Phase Formula | Splicing-Site Phases | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Homo sapiens | SDR7C1 | 122221 | 1 | 2 | 2 | 2 | 2 | 1 | |||||||||||||||||||||||||||||||
SDR7C2 | 1 | 2 | 2 | 2 | 2 | 1 | |||||||||||||||||||||||||||||||||
SDR7C3 | 122222 | 1 | 2 | 2 | 2 | 2 | 2 | ||||||||||||||||||||||||||||||||
SDR7C4 | 0 | 0 | |||||||||||||||||||||||||||||||||||||
SDR7C5 | 2022 | 2 | 0 | 2 | 2 | ||||||||||||||||||||||||||||||||||
SDR40C1 | 120020022 | 1 | 2 | 0 | 0 | 2 | 0 | 0 | 2 | 2 | |||||||||||||||||||||||||||||
Ciona intestinalis | SDR7C-1C1 | 22212 | 2 | 2 | 2 | 1 | 2 | ||||||||||||||||||||||||||||||||
SDR7C-1C2 | 02021 | 0 | 2 | 0 | 2 | 1 | |||||||||||||||||||||||||||||||||
SDR7C-3C2 | 100022 | 1 | 0 | 0 | 2 | 2 | |||||||||||||||||||||||||||||||||
SDR7C-3C3 | 202021 | 2 | 0 | 2 | 0 | 2 | 1 | ||||||||||||||||||||||||||||||||
SDR7C-3C4 | 02021 | 0 | 2 | 0 | 2 | 1 | |||||||||||||||||||||||||||||||||
Strongylocentrotus purpuratus | SDR7C-1C1 | 2221 | 2 | 2 | 2 | 1 | |||||||||||||||||||||||||||||||||
SDR7C-1C3 | 122221 | 1 | 2 | 2 | 2 | 2 | 1 | ||||||||||||||||||||||||||||||||
SDR7C-2C2 | 222 | 2 | 2 | 2 | |||||||||||||||||||||||||||||||||||
Musca domestica | SDR7C-1C3 | 10102 | 1 | 0 | 1 | 0 | 2 | ||||||||||||||||||||||||||||||||
Brugia malayi | SDR7C-1C1 | 2022001 | 2 | 0 | 2 | 2 | 0 | 0 | 1 | ||||||||||||||||||||||||||||||
Aplysia californica | SDR7C-1C2 | 212222 | 2 | 1 | 2 | 2 | 2 | 2 | |||||||||||||||||||||||||||||||
SDR7C-1C3 | 122221 | 1 | 2 | 2 | 2 | 2 | 1 |
Species | Variants | % Identity | |||||
---|---|---|---|---|---|---|---|
Homo sapiens | SDR7C1 | SDR7C2 | SDR7C3 | SDR7C4 | SDR7C5 | SDR40C1 | |
SDR7C2 | 71.66 | ||||||
SDR7C3 | 49.20 | 48.89 | |||||
SDR7C4 | 45.31 | 46.75 | 48.72 | ||||
SDR7C5H | 45.87 | 47.21 | 42.01 | 45.39 | |||
SDR40C1 | 30.20 | 31.00 | 28.05 | 28.72 | 26.33 | ||
Ciona intestinalis | SDR7C-1C1 | 37.26 | 38.78 | 34.46 | 36.31 | 35.62 | 26.40 |
SDR7C-1C2 | 46.05 | 48.11 | 47.68 | 46.08 | 36.79 | 24.64 | |
SDR7C-3C2 | 26.00 | 27.48 | 25.25 | 26.51 | 25.83 | 54.57 | |
SDR7C-3C3 | 36.69 | 35.48 | 33.02 | 32.57 | 34.50 | 25.33 | |
SDR7C-3C4 | 46.25 | 46.93 | 44.73 | 46.91 | 39.54 | 23.67 | |
Strongylocentrotus purpuratus | SDR7C-1C1 | 54.12 | 53.76 | 53.36 | 50.53 | 44.04 | 30.71 |
SDR7C-1C3 | 47.17 | 47.78 | 59.09 | 48.90 | 40.30 | 29.61 | |
SDR7C-2C2 | 42.49 | 42.77 | 42.86 | 42.44 | 45.02 | 27.63 | |
Musca domestica | SDR7C-1C3 | 49.37 | 51.91 | 53.92 | 47.78 | 44.52 | 31.25 |
Brugia malayi | SDR7C-1C1 | 36.77 | 39.48 | 38.54 | 41.40 | 33.66 | 27.67 |
Aplysia californica | SDR7C-1C2 | 39.81 | 41.04 | 41.38 | 36.86 | 33.13 | 29.24 |
SDR7C-1C3 | 49.05 | 46.47 | 52.05 | 47.34 | 40.26 | 28.57 |
Family Symbol and Name | Enzyme Symbol | Gene Symbol | Gene ID | Chr | Exons | Phase Formula | aa n. | % Identity | Structure Consensus | Catalysis Consensus |
---|---|---|---|---|---|---|---|---|---|---|
SDR42E 3-β-HSD family | SDR42E1 | SDR42E1 | 93517 | 16 | 2 | 1 | 393 | 47.18 | GGSGYFG | YSRTK |
SDR42E2 | SDR42E2 | 100288072 | 12 | 20020200020 | 626 | GGGGYLG |
Species | Variants | Phase Formula | Splicing-Site Phases | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
H. sapiens | SDR42E1 | 1 | 1 | |||||||||||||||
SDR42E2 | 0020200020 | 0 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | |||||||
C. intestinalis | SDR42-1E1 | 100202000202 | 1 | 0 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 2 | ||||
S. purpuratus | SDR42-1E1 | 02020020 | 0 | 2 | 0 | 2 | 0 | 0 | 2 | 0 | ||||||||
Caenorhabditis elegans | SDR42-1E1 | 20000 | 2 | 0 | 0 | 0 | 0 | 0 | ||||||||||
SDR42-2E1 | 000000 | 0 | 0 | 0 | 0 | 0 | 0 | |||||||||||
Caenorhabditis remanei | SDR42-1E2 | 00000 | 0 | 0 | 0 | 0 | 0 | |||||||||||
A. californica | SDR42-1E1 | 2000020 | 2 | 0 | 0 | 0 | 0 | 2 | 0 |
Species | Variants | % Identity | |
---|---|---|---|
H sapiens | SDR42E1 | SDR42E2 | |
SDR42E2 | 47.18 | ||
C. intestinalis | SDR42-1E1 | 41.58 | 40.69 |
S. purpuratus | SDR42-1E1 | 49.55 | 43.88 |
C. elegans | SDR42-1E1 | 27.01 | 27.54 |
SDR42-2E1 | 24.72 | 29.46 | |
C. remanei | SDR42-1E2 | 28.33 | 31.58 |
A. californica | SDR42-1E1 | 48.97 | 39.69 |
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Gabrielli, F.; Antinucci, M.; Tofanelli, S. Gene Structure Evolution of the Short-Chain Dehydrogenase/Reductase (SDR) Family. Genes 2023, 14, 110. https://doi.org/10.3390/genes14010110
Gabrielli F, Antinucci M, Tofanelli S. Gene Structure Evolution of the Short-Chain Dehydrogenase/Reductase (SDR) Family. Genes. 2023; 14(1):110. https://doi.org/10.3390/genes14010110
Chicago/Turabian StyleGabrielli, Franco, Marco Antinucci, and Sergio Tofanelli. 2023. "Gene Structure Evolution of the Short-Chain Dehydrogenase/Reductase (SDR) Family" Genes 14, no. 1: 110. https://doi.org/10.3390/genes14010110
APA StyleGabrielli, F., Antinucci, M., & Tofanelli, S. (2023). Gene Structure Evolution of the Short-Chain Dehydrogenase/Reductase (SDR) Family. Genes, 14(1), 110. https://doi.org/10.3390/genes14010110