Gene
prkdc
- ID
- ZDB-GENE-030131-9008
- Name
- protein kinase, DNA-activated, catalytic subunit
- Symbol
- prkdc Nomenclature History
- Previous Names
-
- fa96e12
- wu:fa96e12 (1)
- Type
- protein_coding_gene
- Location
- Chr: 7 Mapping Details/Browsers
- Description
- Predicted to enable protein serine/threonine kinase activity. Acts upstream of or within B cell differentiation; T cell receptor V(D)J recombination; and immunoglobulin heavy chain V-D-J recombination. Predicted to be located in nucleolus. Predicted to be active in nucleus. Is expressed in kidney and spleen. Used to study severe combined immunodeficiency. Human ortholog(s) of this gene implicated in immunodeficiency 26. Orthologous to human PRKDC (protein kinase, DNA-activated, catalytic subunit).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 3 figures from 3 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
-
- IMAGE:7147291 (1 image)
Wild Type Expression Summary
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| fb103 | Allele with one deletion | Unknown | Frameshift, Premature Stop | TALEN | |
| ihb478 | Allele with one deletion | Exon 7 | Unknown | CRISPR | |
| sa903 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa978 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa7082 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa12418 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa13311 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa13548 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa16262 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa17162 | Allele with one point mutation | Unknown | Premature Stop | ENU |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-prkdc | (2) | |
| CRISPR2-prkdc | Wu et al., 2022 | |
| CRISPR3-prkdc | Zebrafish Nomenclature Committee | |
| TALEN1-prkdc | Jung et al., 2016 | |
| TALEN2-prkdc | (8) |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| immunodeficiency 26 | Alliance | Immunodeficiency 26, with or without neurologic abnormalities | 615966 |
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| Human Disease | Fish | Conditions | Citations |
|---|---|---|---|
| severe combined immunodeficiency | prkdcyu27/yu27 (AB) | standard conditions | Jung et al., 2016 |
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Domain, Family, and Site Summary
| Type | InterPro ID | Name |
|---|---|---|
| Conserved_site | IPR018936 | Phosphatidylinositol 3/4-kinase, conserved site |
| Domain | IPR000403 | Phosphatidylinositol 3-/4-kinase, catalytic domain |
| Domain | IPR003151 | PIK-related kinase, FAT |
| Domain | IPR003152 | FATC domain |
| Domain | IPR012582 | DNA-dependent protein kinase catalytic subunit, CC3 |
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Domain Details Per Protein
| Protein | Additional Resources | Length | Armadillo-type fold | DNA Damage Response and Repair Kinase | DNA-dependent protein kinase catalytic subunit, catalytic domain | DNA-dependent protein kinase catalytic subunit, CC1/2 | DNA-dependent protein kinase catalytic subunit, CC3 | DNA-dependent protein kinase catalytic subunit, CC5 | DNA-PKcs, N-terminal | FATC domain | Phosphatidylinositol 3-/4-kinase, catalytic domain | Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily | Phosphatidylinositol 3/4-kinase, conserved site | PIK-related kinase | PIK-related kinase, FAT | Protein kinase-like domain superfamily |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| UniProtKB:E7F4J7 | InterPro | 4119 |
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Interactions and Pathways
No data available
Plasmids
No data available
No data available
| Relationship | Marker Type | Marker | Accession Numbers | Citations |
|---|---|---|---|---|
| Contained in | BAC | CH211-198H5 | ZFIN Curated Data | |
| Contained in | BAC | DKEY-86L18 | ZFIN Curated Data | |
| Encodes | EST | fa96e12 | ||
| Encodes | EST | IMAGE:7147291 | Thisse et al., 2004 |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:XM_009303401 (1) | 12725 nt | ||
| Genomic | GenBank:CT574559 (1) | 110868 nt | ||
| Polypeptide | UniProtKB:E7F4J7 (1) | 4119 aa |
- Zebrafish Nomenclature Committee (2024) Nomenclature Data Curation (2024). Nomenclature Committee Submission.
- Vaz-Rodrigues, R., Mazuecos, L., Villar, M., Contreras, M., Artigas-Jerónimo, S., González-García, A., Gortázar, C., de la Fuente, J. (2023) Multi-omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha-Gal syndrome. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie. 168:115829115829
- Solman, M., Blokzijl-Franke, S., Piques, F., Yan, C., Yang, Q., Strullu, M., Kamel, S.M., Ak, P., Bakkers, J., Langenau, D.M., Cave, H., den Hertog, J. (2022) Inflammatory response in hematopoietic stem and progenitor cells triggered by activating SHP2 mutations evokes blood defects. eLIFE. 11:
- Wu, C., Hu, B., Wang, L., Wu, X., Gu, H., Dong, H., Yan, J., Qi, Z., Zhang, Q., Chen, H., Yu, B., Hu, S., Qian, Y., Dong, S., Li, Q., Wang, X., Long, J. (2022) Assessment of stromal SCD-induced drug resistance of PDAC using 3D-printed zPDX model chips. iScience. 26:105723105723
- Somasagara, R.R., Huang, X., Xu, C., Haider, J., Serody, J.S., Armistead, P.M., Leung, T. (2021) Targeted therapy of human leukemia xenografts in immunodeficient zebrafish. Scientific Reports. 11:5715
- Yan, C., Do, D., Yang, Q., Brunson, D.C., Rawls, J.F., Langenau, D.M. (2020) Single-cell imaging of human cancer xenografts using adult immunodeficient zebrafish. Nature Protocols. 15(9):3105-3128
- Bian, W.P., Chen, Y., Luo, J., Wang, C., Xie, S., Pei, D. (2019) A knock-in strategy for editing human and zebrafish mitochondrial DNA using mito-CRISPR/Cas9 system. ACS synthetic biology. 8(4):621-632
- Yan, C., Brunson, D.C., Tang, Q., Do, D., Iftimia, N.A., Moore, J.C., Hayes, M.N., Welker, A.M., Garcia, E.G., Dubash, T.D., Hong, X., Drapkin, B.J., Myers, D.T., Phat, S., Volorio, A., Marvin, D.L., Ligorio, M., Dershowitz, L., McCarthy, K.M., Karabacak, M.N., Fletcher, J.A., Sgroi, D.C., Iafrate, J.A., Maheswaran, S., Dyson, N.J., Haber, D.A., Rawls, J.F., Langenau, D.M. (2019) Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish. Cell. 177(7):1903-1914.e14
- Bayés, À., Collins, M.O., Reig-Viader, R., Gou, G., Goulding, D., Izquierdo, A., Choudhary, J.S., Emes, R.D., Grant, S.G. (2017) Evolution of complexity in the zebrafish synapse proteome. Nature communications. 8:14613
- Benjamin, D.C., Hynes, R.O. (2017) Intravital imaging of metastasis in adult Zebrafish. BMC cancer. 17:660
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