Gene
kdm6a
- ID
- ZDB-GENE-081105-56
- Name
- lysine (K)-specific demethylase 6A
- Symbol
- kdm6a Nomenclature History
- Previous Names
-
- si:ch211-222m21.1
- utx-a (1)
- Type
- protein_coding_gene
- Location
- Chr: 9 Mapping Details/Browsers
- Description
- Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; chromatin DNA binding activity; and histone H3K27me2/H3K27me3 demethylase activity. Acts upstream of or within several processes, including embryonic morphogenesis; face development; and germ cell migration. Predicted to be located in nucleus. Predicted to be part of MLL3/4 complex. Is expressed in several structures, including blood island; ethmoid cartilage; otic vesicle; pharyngeal arch; and pronephric duct. Used to study Kabuki syndrome. Human ortholog(s) of this gene implicated in several diseases, including Kabuki syndrome; bladder urothelial carcinoma; gastrointestinal system cancer (multiple); lung carcinoma (multiple); and triple-receptor negative breast cancer. Orthologous to human KDM6A (lysine demethylase 6A).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 4 figures from 4 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
- No data available
Wild Type Expression Summary
- All Phenotype Data
- 11 figures from 5 publications
- Cross-Species Comparison
- Alliance
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| la010166Tg | Transgenic insertion | Unknown | Unknown | DNA | |
| la026932Tg | Transgenic insertion | Unknown | Unknown | DNA | |
| la026933Tg | Transgenic insertion | Unknown | Unknown | DNA | |
| la029585Tg | Transgenic insertion | Unknown | Unknown | DNA | |
| sa7197 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa17907 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa34686 | Allele with one point mutation | Unknown | Premature Stop | ENU |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-kdm6a | (3) | |
| MO1-kdm6a | N/A | (2) |
| MO2-kdm6a | N/A | (3) |
| MO3-kdm6a | N/A | Van Laarhoven et al., 2015 |
| MO4-kdm6a | N/A | Van Laarhoven et al., 2015 |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| Kabuki syndrome | Alliance | Kabuki syndrome 2 | 300867 |
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| Human Disease | Fish | Conditions | Citations |
|---|---|---|---|
| Kabuki syndrome | EKW + MO2-kdm6a | standard conditions | Tsai et al., 2018 |
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Domain, Family, and Site Summary
| Type | InterPro ID | Name |
|---|---|---|
| Domain | IPR003347 | JmjC domain |
| Domain | IPR048560 | Lysine-specific demethylase 6A/B-like, GATA-like |
| Domain | IPR048562 | Lysine-specific demethylase 6A/B-like, C-terminal helical domain |
| Family | IPR051630 | Transcriptional Corepressor and Histone Demethylase |
| Homologous_superfamily | IPR011990 | Tetratricopeptide-like helical domain superfamily |
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Domain Details Per Protein
| Protein | Additional Resources | Length | JmjC domain | Lysine-specific demethylase 6A/B-like, C-terminal helical domain | Lysine-specific demethylase 6A/B-like, GATA-like | Lysine-specific demethylase 6, GATA-like domain superfamily | Tetratricopeptide-like helical domain superfamily | Tetratricopeptide repeat | Transcriptional Corepressor and Histone Demethylase |
|---|---|---|---|---|---|---|---|---|---|
| UniProtKB:F1Q597 | InterPro | 1452 | |||||||
| UniProtKB:A0A8M2BF83 | InterPro | 1248 | |||||||
| UniProtKB:A0A8M2BFV4 | InterPro | 1437 | |||||||
| UniProtKB:A0A8M6Z877 | InterPro | 1407 |
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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 | CH73-147F11 | ZFIN Curated Data | |
| Contained in | BAC | CH211-222M21 | ZFIN Curated Data |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:XM_005167794 (1) | 5812 nt | ||
| Genomic | GenBank:BX572627 (1) | 209758 nt | ||
| Polypeptide | UniProtKB:F1Q597 (1) | 1452 aa |
- 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
- Tsai, I.C., McKnight, K., McKinstry, S.U., Maynard, A.T., Tan, P.L., Golzio, C., White, C.T., Price, D.J., Davis, E.E., Amrine-Madsen, H., Katsanis, N. (2018) Small molecule inhibition of RAS/MAPK signaling ameliorates developmental pathologies of Kabuki Syndrome. Scientific Reports. 8:10779
- Wu, X., Shen, W., Zhang, B., Meng, A. (2018) The genetic program of oocytes can be modified in vivo in the zebrafish ovary. Journal of molecular cell biology. 10(6):479-493
- Yu, S.H., Zhu, K.Y., Zhang, F., Wang, J., Yuan, H., Chen, Y., Jin, Y., Dong, M., Wang, L., Jia, X.E., Gao, L., Dong, Z.W., Ren, C.G., Chen, L.T., Huang, Q.H., Deng, M., Zon, L.I., Zhou, Y., Zhu, J., Xu, P.F., Liu, T.X. (2018) The histone demethylase Jmjd3 regulates zebrafish myeloid development by promoting spi1 expression. Biochimica et biophysica acta. 1861(2):106-116
- Akerberg, A.A., Henner, A., Stewart, S., Stankunas, K. (2017) Histone demethylases Kdm6ba and Kdm6bb redundantly promote cardiomyocyte proliferation during zebrafish heart ventricle maturation. Developmental Biology. 426(1):84-96
- Heid, J., Cencioni, C., Ripa, R., Baumgart, M., Atlante, S., Milano, G., Scopece, A., Kuenne, C., Guenther, S., Azzimato, V., Farsetti, A., Rossi, G., Braun, T., Pompilio, G., Martelli, F., Zeiher, A.M., Cellerino, A., Gaetano, C., Spallotta, F. (2017) Age-dependent increase of oxidative stress regulates microRNA-29 family preserving cardiac health. Scientific Reports. 7:16839
- Bögershausen, N., Tsai, I.C., Pohl, E., Kiper, P.Ö., Beleggia, F., Percin, E.F., Keupp, K., Matchan, A., Milz, E., Alanay, Y., Kayserili, H., Liu, Y., Banka, S., Kranz, A., Zenker, M., Wieczorek, D., Elcioglu, N., Prontera, P., Lyonnet, S., Meitinger, T., Stewart, A.F., Donnai, D., Strom, T.M., Boduroglu, K., Yigit, G., Li, Y., Katsanis, N., Wollnik, B. (2015) RAP1-mediated MEK/ERK pathway defects in Kabuki syndrome. The Journal of Clinical Investigation. 125(9):3585-99
- 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
- Van Laarhoven, P.M., Neitzel, L.R., Quintana, A.M., Geiger, E.A., Zackai, E.H., Clouthier, D.E., Artinger, K.B., Ming, J.E., Shaikh, T.H. (2015) Kabuki syndrome genes KMT2D and KDM6A: functional analyses demonstrate critical roles in craniofacial, heart, and brain development. Human molecular genetics. 24(15):4443-53
- Gagnon, J.A., Valen, E., Thyme, S.B., Huang, P., Ahkmetova, L., Pauli, A., Montague, T.G., Zimmerman, S., Richter, C., Schier, A.F. (2014) Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs. PLoS One. 9:e98186
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