Genomic Identification and Expression Analysis of Regulator of Chromosome Condensation 1-Domain Protein Family in Maize
Abstract
1. Introduction
2. Results
2.1. Identification and Prediction of Protein Physicochemical Properties
2.2. Phylogenetic Relationship and Collinearity Analysis
2.3. Conserved Motifs, Domains, and Gene Structure Analysis
2.4. Distribution of ZmRCP Family Members on Chromosomes
2.5. Subcellular Localization of ZmRCP Family Members
2.6. Prediction of Cis-Elements in the Promoters
2.7. Analysis of Expression Patterns under Different Tissues and Stresses
2.8. Prediction of Protein Interaction Network
3. Discussion
4. Materials and Methods
4.1. Materials and Treatments
4.2. Identification of RCP Family Members
4.3. Construction of Phylogenetic Tree
4.4. Collinearity Analysis
4.5. Analysis of Cis-Acting Elements in the Promoters
4.6. Prediction of Protein Physicochemical Properties
4.7. Gene Structure, Conserved Motif, and Structural Domain Analysis
4.8. Location on Chromosome
4.9. Expression Pattern Analysis
4.10. Subcellular Localization
4.11. Analysis of Protein Interaction Network Prediction
4.12. RT-qPCR
4.13. Yeast Two-Hybrid Assay
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | Protein Name | Subcellular Localization | Protein Length/aa | Molecular Mass/Da | Theoretical pI | Instability Index | Grand Average of Hydropathicity |
---|---|---|---|---|---|---|---|
Zm00001eb016900 | ZmRCP1 | Chloroplast | 371 | 41,019.26 | 4.95 | 35.26 | −0.308 |
Zm00001eb041760 | ZmRCP2 | Nucleus | 427 | 45,901.78 | 8.38 | 28.27 | −0.349 |
Zm00001eb049950 | ZmRCP3 | Nucleus | 480 | 51,477.95 | 5.94 | 30.7 | −0.206 |
Zm00001eb072860 | ZmRCP4 | Nucleus | 1073 | 118,737.65 | 9.00 | 37.37 | −0.468 |
Zm00001eb075990 | ZmRCP5/ZmRLD1 | Nucleus | 1060 | 115,768.8 | 8.47 | 41.97 | −0.458 |
Zm00001eb082500 | ZmRCP6/ZmRCC1-2 | Nucleus | 443 | 47,158.43 | 5.38 | 37.24 | −0.346 |
Zm00001eb096520 | ZmRCP7 | Cell wall, nucleus | 483 | 51,229.18 | 6.62 | 27.16 | −0.010 |
Zm00001eb140790 | ZmRCP8/ZmRLD4 | Chloroplast, nucleus | 1091 | 118,047.68 | 8.89 | 43.98 | −0.448 |
Zm00001eb148070 | ZmRCP9/ZmRCC1-1 | Nucleus | 503 | 51,936.8 | 5.43 | 45.05 | −0.263 |
Zm00001eb151590 | ZmRCP10 | Nucleus | 404 | 43,284.09 | 5.59 | 29.71 | −0.230 |
Zm00001eb153510 | ZmRCP11 | Cell wall, nucleus | 200 | 21,328.17 | 9.84 | 6.81 | −0.177 |
Zm00001eb154440 | ZmRCP12 | Nucleus | 416 | 45,496.38 | 5.21 | 43.89 | −0.181 |
Zm00001eb179510 | ZmRCP13/ZmRCC1-3 | Nucleus | 389 | 41,874.04 | 6.01 | 28.34 | −0.351 |
Zm00001eb183880 | ZmRCP14 | Cell wall, mitochondrion | 535 | 57,269.85 | 5.65 | 32.71 | −0.093 |
Zm00001eb187440 | ZmRCP15 | Nucleus | 1067 | 117,523.14 | 8.91 | 43.04 | −0.475 |
Zm00001eb188870 | ZmRCP16 | Nucleus | 181 | 19,246.71 | 8.54 | 19.79 | −0.118 |
Zm00001eb196450 | ZmRCP17 | Nucleus | 448 | 49,266.91 | 9.51 | 24.39 | −0.031 |
Zm00001eb197640 | ZmRCP18 | Nucleus | 462 | 49,028.32 | 6.40 | 43.18 | −0.102 |
Zm00001eb205920 | ZmRCP19 | Nucleus | 442 | 46,469.45 | 5.70 | 36.51 | −0.034 |
Zm00001eb250930 | ZmRCP20 | Nucleus | 784 | 86,289.9 | 8.85 | 39.96 | −0.506 |
Zm00001eb267290 | ZmRCP21/ZmRLD2 | Nucleus | 917 | 99,449.7 | 8.51 | 35.57 | −0.400 |
Zm00001eb294600 | ZmRCP22 | Nucleus | 1009 | 109,869.18 | 8.83 | 42.92 | −0.407 |
Zm00001eb300770 | ZmRCP23 | Nucleus | 1078 | 116,042.22 | 9.12 | 42.32 | −0.447 |
Zm00001eb306630 | ZmRCP24 | Cell wall, nucleus | 483 | 51,361.1 | 6.52 | 29.82 | −0.048 |
Zm00001eb320310 | ZmRCP25/DEK47 | mitochondria | 432 | 45,433.14 | 6.49 | 36.49 | −0.153 |
Zm00001eb360990 | ZmRCP26 | Nucleus | 1054 | 115,204.69 | 8.71 | 39.45 | −0.482 |
Zm00001eb362420 | ZmRCP27/ZmRLD3 | Nucleus | 912 | 98,988.94 | 8.70 | 46.22 | −0.470 |
Zm00001eb362840 | ZmRCP28/ZmRLD5 | Nucleus | 1092 | 117,959.71 | 8.95 | 43.31 | −0.445 |
Zm00001eb367810 | ZmRCP29 | Nucleus | 588 | 61,993.36 | 6.22 | 49.16 | −0.350 |
Zm00001eb432950 | ZmRCP30 | Cell wall, nucleus | 549 | 58,115.71 | 8.42 | 38.59 | −0.609 |
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Liu, R.; Ma, T.; Li, Y.; Lei, X.; Ji, H.; Du, H.; Zhang, J.; Cao, S.-K. Genomic Identification and Expression Analysis of Regulator of Chromosome Condensation 1-Domain Protein Family in Maize. Int. J. Mol. Sci. 2024, 25, 11437. https://doi.org/10.3390/ijms252111437
Liu R, Ma T, Li Y, Lei X, Ji H, Du H, Zhang J, Cao S-K. Genomic Identification and Expression Analysis of Regulator of Chromosome Condensation 1-Domain Protein Family in Maize. International Journal of Molecular Sciences. 2024; 25(21):11437. https://doi.org/10.3390/ijms252111437
Chicago/Turabian StyleLiu, Rui, Tian Ma, Yu Li, Xiongbiao Lei, Hongjing Ji, Hewei Du, Jianhua Zhang, and Shi-Kai Cao. 2024. "Genomic Identification and Expression Analysis of Regulator of Chromosome Condensation 1-Domain Protein Family in Maize" International Journal of Molecular Sciences 25, no. 21: 11437. https://doi.org/10.3390/ijms252111437
APA StyleLiu, R., Ma, T., Li, Y., Lei, X., Ji, H., Du, H., Zhang, J., & Cao, S.-K. (2024). Genomic Identification and Expression Analysis of Regulator of Chromosome Condensation 1-Domain Protein Family in Maize. International Journal of Molecular Sciences, 25(21), 11437. https://doi.org/10.3390/ijms252111437