Gene
setd2
- ID
- ZDB-GENE-030131-2140
- Name
- SET domain containing 2, histone lysine methyltransferase
- Symbol
- setd2 Nomenclature History
- Previous Names
-
- fb97h09
- wu:fb97h09 (1)
- Type
- protein_coding_gene
- Location
- Chr: 16 Mapping Details/Browsers
- Description
- Enables histone H3K36 methyltransferase activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within methylation. Predicted to be active in chromosome and nucleus. Is expressed in central nervous system; intermediate cell mass of mesoderm; and telencephalon. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 70; clear cell renal cell carcinoma; gastrointestinal system cancer (multiple); lung disease (multiple); and malignant mesothelioma (multiple). Orthologous to human SETD2 (SET domain containing 2, histone lysine methyltransferase).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 4 figures from 3 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
- No data available
Wild Type Expression Summary
- All Phenotype Data
- 5 figures from Liu et al., 2020
- Cross-Species Comparison
- Alliance
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| rj33 | Allele with one delins | Exon 3 | Frameshift | CRISPR | |
| rj34 | Allele with one deletion | Exon 3 | Unknown | CRISPR | |
| rj35 | Allele with one delins | Exon 19 | Frameshift | CRISPR | |
| sa678 | Allele with one point mutation | Unknown | Unknown | ENU | |
| sa9194 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa22792 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa25011 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa36079 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa39086 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa42691 | Allele with one point mutation | Unknown | Premature Stop | ENU |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-setd2 | Liu et al., 2020 | |
| CRISPR2-setd2 | Liu et al., 2020 | |
| CRISPR3-setd2 | Lin et al., 2025 | |
| CRISPR4-setd2 | Lin et al., 2025 | |
| MO1-setd2 | N/A | (2) |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| autosomal dominant intellectual developmental disorder 70 | Alliance | Intellectual developmental disorder, autosomal dominant 70 | 620157 |
| Luscan-Lumish syndrome | 616831 | ||
| Rabin-Pappas syndrome | 620155 |
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Domain, Family, and Site Summary
Domain Details Per Protein
| Protein | Additional Resources | Length | AWS domain | Histone-lysine N-methyltransferase SETD2, animal | Post-SET domain | Set2 Rpb1 interacting domain | Set2 Rpb1 interacting domain superfamily | SETD2/Set2, SET domain | SET domain | SET domain superfamily | WW domain | WW domain superfamily |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| UniProtKB:A0A8M9PJZ4 | InterPro | 2723 | ||||||||||
| UniProtKB:F1QJI9 | InterPro | 2737 |
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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 | CH211-193P21 | ||
| Contained in | BAC | DKEY-43F15 | ZFIN Curated Data | |
| Contains | SNP | rs3728778 | ||
| Contains | SNP | rs3728779 | ZFIN Curated Data | |
| Contains | SNP | rs3728780 | ZFIN Curated Data | |
| Contains | SNP | rs3728781 | ZFIN Curated Data | |
| Encodes | EST | fb97h09 |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:XM_009292184 (1) | 9914 nt | ||
| Genomic | GenBank:CU138519 (2) | 93287 nt | ||
| Polypeptide | UniProtKB:F1QJI9 (1) | 2737 aa |
- Lin, S.J., Huang, K., Petree, C., Qin, W., Varshney, P., Varshney, G.K. (2025) Optimizing gRNA selection for high-penetrance F0 CRISPR screening for interrogating disease gene function. Nucleic acids research. 53:
- Calvird, A.E., Broniec, M.N., Duval, K.L., Higgs, A.N., Arora, V., Ha, L.N., Schouten, E.B., Crippen, A.R., McGrail, M., Laue, K., Goll, M.G. (2022) Uncovering Regulators of Heterochromatin Mediated Silencing Using a Zebrafish Transgenic Reporter. Frontiers in cell and developmental biology. 10:832461
- Gabellini, C., Pucci, C., De Cesari, C., Martini, D., Di Lauro, C., Digregorio, M., Norton, W., Zippo, A., Sessa, A., Broccoli, V., Andreazzoli, M. (2022) CRISPR/Cas9-Induced Inactivation of the Autism-Risk Gene setd5 Leads to Social Impairments in Zebrafish. International Journal of Molecular Sciences. 24(1):
- Liu, D.J., Zhang, F., Chen, Y., Jin, Y., Zhang, Y.L., Chen, S.B., Xie, Y.Y., Huang, Q.H., Zhao, W.L., Wang, L., Xu, P.F., Chen, Z., Chen, S.J., Li, B., Zhang, A., Sun, X.J. (2020) setd2 knockout zebrafish is viable and fertile: differential and developmental stress-related requirements for Setd2 and histone H3K36 trimethylation in different vertebrate animals. Cell discovery. 6:72
- Fellous, A., Earley, R.L., Silvestre, F. (2018) The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Gene. 687:173-187
- Diotel, N., Viales, R.R., Armant, O., März, M., Ferg, M., Rastegar, S., Strähle, U. (2015) Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. The Journal of comparative neurology. 523(8):1202-21
- Elkon, R., Milon, B., Morrison, L., Shah, M., Vijayakumar, S., Racherla, M., Leitch, C.C., Silipino, L., Hadi, S., Weiss-Gayet, M., Barras, E., Schmid, C.D., Ait-Lounis, A., Barnes, A., Song, Y., Eisenman, D.J., Eliyahu, E., Frolenkov, G.I., Strome, S.E., Durand, B., Zaghloul, N.A., Jones, S.M., Reith, W., Hertzano, R. (2015) RFX transcription factors are essential for hearing in mice. Nature communications. 6:8549
- Huang, H.T., Kathrein, K.L., Barton, A., Gitlin, Z., Huang, Y.H., Ward, T.P., Hofmann, O., Dibiase, A., Song, A., Tyekucheva, S., Hide, W., Zhou, Y., and Zon, L.I. (2013) A network of epigenetic regulators guides developmental haematopoiesis in vivo. Nature cell biology. 15(12):1516-1525
- Sun, X.J., Xu, P.F., Zhou, T., Hu, M., Fu, C.T., Zhang, Y., Jin, Y., Chen, Y., Chen, S.J., Huang, Q.H., Liu, T.X., and Chen, Z. (2008) Genome-Wide Survey and Developmental Expression Mapping of Zebrafish SET Domain-Containing Genes. PLoS One. 3(1):e1499
- Woods, I.G., Wilson, C., Friedlander, B., Chang, P., Reyes, D.K., Nix, R., Kelly, P.D., Chu, F., Postlethwait, J.H., and Talbot, W.S. (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome research. 15(9):1307-1314
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