Gene
kdm6ba
- ID
- ZDB-GENE-091005-1
- Name
- lysine (K)-specific demethylase 6B, a
- Symbol
- kdm6ba Nomenclature History
- Previous Names
-
- jmjd3b (1)
- Type
- protein_coding_gene
- Location
- Chr: 7 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 heart development and heart trabecula morphogenesis. Predicted to be located in nucleus. Predicted to be part of MLL3/4 complex. Is expressed in brain; heart; and otic vesicle. Human ortholog(s) of this gene implicated in Stolerman neurodevelopmental syndrome. Orthologous to human KDM6B (lysine demethylase 6B).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 5 figures from 3 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
- No data available
Wild Type Expression Summary
- All Phenotype Data
- 1 Figure from Akerberg et al., 2017
- Cross-Species Comparison
- Alliance
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| b1308 | Allele with one deletion | Exon 14 | Frameshift, Premature Stop | CRISPR | |
| sa8805 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa16587 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa18869 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa26939 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa40872 | Allele with one point mutation | Unknown | Splice Site | ENU |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-kdm6ba | Akerberg et al., 2017 | |
| MO1-kdm6ba | N/A | Huang et al., 2013 |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| Stolerman neurodevelopmental syndrome | Alliance | Stolerman neurodevelopmental syndrome | 618505 |
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 | IPR046941 | Lysine-specific demethylase 6, GATA-like domain superfamily |
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 | Transcriptional Corepressor and Histone Demethylase |
|---|---|---|---|---|---|---|---|
| UniProtKB:A0A8M3AU53 | InterPro | 1996 |
| Type | Name | Annotation Method | Has Havana Data | Length (nt) | Analysis |
|---|---|---|---|---|---|
| mRNA |
kdm6ba-201
(1)
|
Ensembl | 1,578 nt | ||
| mRNA |
kdm6ba-203
(1)
|
Ensembl | 8,578 nt | ||
| ncRNA |
kdm6ba-002
(1)
|
Ensembl | 855 nt | ||
| ncRNA |
kdm6ba-003
(1)
|
Ensembl | 706 nt |
Interactions and Pathways
No data available
Plasmids
No data available
No data available
| Relationship | Marker Type | Marker | Accession Numbers | Citations |
|---|---|---|---|---|
| Contained in | BAC | CH211-262E4 | ZFIN Curated Data | |
| Contained in | BAC | CH211-265E16 | ZFIN Curated Data | |
| Contained in | BAC | DKEY-46E6 | ||
| Contained in | BAC | DKEY-85K7 |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:XM_009303125 (1) | 8819 nt | ||
| Genomic | GenBank:BX005336 (1) | 233826 nt | ||
| Polypeptide | UniProtKB:A0A8M3AU53 (1) | 1996 aa |
- Comparative Orthology
- Alliance
- Dennhag, N., Kahsay, A., Nissen, I., Nord, H., Chermenina, M., Liu, J., Arner, A., Liu, J.X., Backman, L.J., Remeseiro, S., von Hofsten, J., Pedrosa Domellöf, F. (2024) fhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles. Nature communications. 15:19501950
- Cheung, C.T., Nguyen, T.V., Le Cam, A., Patinote, A., Journot, L., Reynes, C., Bobe, J. (2019) What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization. BMC Genomics. 20:584
- 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
- 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
- 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
- Ferreira, T., Wilson, S.R., Choi, Y.G., Risso, D., Dudoit, S., Speed, T.P., Ngai, J. (2014) Silencing of Odorant Receptor Genes by G Protein βγ Signaling Ensures the Expression of One Odorant Receptor per Olfactory Sensory Neuron. Neuron. 81(4):847-59
- 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
- Kassahn, K.S., Dang, V.T., Wilkins, S.J., Perkins, A.C., and Ragan, M.A. (2009) Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates. Genome research. 19(8):1404-1418
- Stewart, S., Tsun, Z.Y., and Izpisúa Belmonte, J.C. (2009) A histone demethylase is necessary for regeneration in zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 106(47):19889-19894
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