Gene
smarca4a
- ID
- ZDB-GENE-030605-1
- Name
- SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4a
- Symbol
- smarca4a Nomenclature History
- Previous Names
- Type
- protein_coding_gene
- Location
- Chr: 3 Mapping Details/Browsers
- Description
- Predicted to enable DNA binding activity; chromatin binding activity; and nucleosome array spacer activity. Acts upstream of or within several processes, including camera-type eye development; heart development; and nervous system development. Predicted to be part of SWI/SNF complex. Predicted to be active in chromatin and nucleus. Is expressed in several structures, including hematopoietic multipotent progenitor cell; mesoderm; nervous system; pectoral fin; and presumptive neural retina. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid tumor predisposition syndrome 2. Orthologous to human SMARCA4 (SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 21 figures from 10 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
-
- IMAGE:5611934 (1 image)
- IMAGE:6909706 (1 image)
- IMAGE:7138284 (1 image)
- ay205256 (17 images)
Wild Type Expression Summary
- All Phenotype Data
- 24 figures from 10 publications
- Cross-Species Comparison
- Alliance
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| a8 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| a50 | Allele with one point mutation | Unknown | Unknown | ENU | |
| hzu13 | Allele with one delins | Exon 1 | Unknown | TALEN | |
| s481 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa12514 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa19981 | Allele with one point mutation | Unknown | Splice Site | ENU |
1 - 6 of 6
Show
| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| MO1-smarca4a | N/A | (5) |
| MO2-smarca4a | N/A | Gregg et al., 2003 |
| MO3-smarca4a | N/A | (2) |
| TALEN1-smarca4a | Tu et al., 2020 |
1 - 4 of 4
Show
Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| Coffin-Siris syndrome 4 | Alliance | Coffin-Siris syndrome 4 | 614609 |
| rhabdoid tumor predisposition syndrome 2 | Alliance | {Rhabdoid tumor predisposition syndrome 2} | 613325 |
| ?Otosclerosis 12 | 620792 |
Domain, Family, and Site Summary
| Type | InterPro ID | Name |
|---|---|---|
| Conserved_site | IPR018359 | Bromodomain, conserved site |
| Domain | IPR000330 | SNF2, N-terminal |
| Domain | IPR001487 | Bromodomain |
| Domain | IPR001650 | Helicase, C-terminal domain-like |
| Domain | IPR006576 | BRK domain |
| Domain | IPR014001 | Helicase superfamily 1/2, ATP-binding domain |
| Domain | IPR014012 | Helicase/SANT-associated domain |
| Domain | IPR014978 | Glutamine-Leucine-Glutamine, QLQ |
| Domain | IPR029295 | Snf2, ATP coupling domain |
| Domain | IPR030100 | SWI/SNF complex subunit BRG1, ATP-binding |
| Domain | IPR049730 | SNF2/RAD5-like, C-terminal helicase domain |
| Homologous_superfamily | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| Homologous_superfamily | IPR036427 | Bromodomain-like superfamily |
| Homologous_superfamily | IPR037259 | BRK domain superfamily |
| Homologous_superfamily | IPR038718 | SNF2-like, N-terminal domain superfamily |
Domain Details Per Protein
| Protein | Length | BRK domain | BRK domain superfamily | Bromodomain | Bromodomain, conserved site | Bromodomain-like superfamily | Glutamine-Leucine-Glutamine, QLQ | Helicase, C-terminal domain-like | Helicase/SANT-associated domain | Helicase superfamily 1/2, ATP-binding domain | P-loop containing nucleoside triphosphate hydrolase | Snf2, ATP coupling domain | SNF2-like, N-terminal domain superfamily | SNF2, N-terminal | SNF2/RAD5-like, C-terminal helicase domain | SWI/SNF complex subunit BRG1, ATP-binding |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
UniProtKB:Q7ZSY3
|
1627 |
| Type | Name | Annotation Method | Has Havana Data | Length (nt) | Analysis |
|---|---|---|---|---|---|
| mRNA |
smarca4a-201
(1)
|
Ensembl | 5,680 nt | ||
| mRNA |
smarca4a-202
(1)
|
Ensembl | 6,220 nt |
Interactions and Pathways
No data available
Plasmids
No data available
| Construct | Regulatory Region | Coding Sequence | Species | Tg Lines | Citations |
|---|---|---|---|---|---|
| Tg(ubb:LOXP-DsRed-LOXP-smarca4a) |
| 1 | Xiao et al., 2016 |
1 - 1 of 1
Show
| Relationship | Marker Type | Marker | Accession Numbers | Citations |
|---|---|---|---|---|
| Contained in | BAC | CH211-224D23 | ZFIN Curated Data | |
| Contains | SNP | rs3727693 | ZFIN Curated Data | |
| Encodes | EST | ay205256 | (2) | |
| Encodes | EST | fb51a08 | ||
| Encodes | EST | IMAGE:5611934 | Thisse et al., 2004 | |
| Encodes | EST | IMAGE:6909706 | Thisse et al., 2004 | |
| Encodes | EST | IMAGE:7138284 | Thisse et al., 2004 | |
| Encodes | cDNA | MGC:77219 | ZFIN Curated Data | |
| Encodes | cDNA | MGC:195345 | ZFIN Curated Data | |
| Encodes | cDNA | MGC:195348 | ZFIN Curated Data |
1 - 10 of 10
Show
| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:NM_181603 (1) | 4884 nt | ||
| Genomic | GenBank:BX322663 (1) | 145520 nt | ||
| Polypeptide | UniProtKB:Q7ZSY3 (1) | 1627 aa |
- Maili, L., Ruiz, O.E., Kahan, P., Chiu, F., Larson, S.T., Hashmi, S.S., Hecht, J.T., Eisenhoffer, G.T. (2023) zFACE: facial analytics from a coordinate extrapolation system for morphometric phenotyping of developing zebrafish. Disease models & mechanisms. 16(6):
- Shull, L.C., Lencer, E.S., Kim, H.M., Goyama, S., Kurokawa, M., Costello, J.C., Jones, K., Artinger, K.B. (2022) PRDM paralogs antagonistically balance Wnt/β-catenin activity during craniofacial chondrocyte differentiation. Development (Cambridge, England). 149(4):
- Zhou, Q., Lei, L., Zhang, H., Chiu, S.C., Gao, L., Yang, R., Wei, W., Peng, G., Zhu, X., Xiong, J.W. (2021) Proprotein Convertase Furina Is Required for Heart Development in Zebrafish. Journal of Cell Science. 134(21):
- Ding, Y., Wang, W., Ma, D., Liang, G., Kang, Z., Xue, Y., Zhang, Y., Wang, L., Heng, J., Zhang, Y., Liu, F. (2020) Smarca5 mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Blood. 137(2):190-202
- Tu, J., Liu, X., Jia, H., Reilly, J., Yu, S., Cai, C., Liu, F., Lv, Y., Huang, Y., Lu, Z., Han, S., Jiang, T., Shu, X., Wu, X., Tang, Z., Lu, Q., Liu, M. (2020) The chromatin remodeler Brg1 is required for formation and maintenance of hematopoietic stem cells. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 34(9):11997-12008
- Dooley, C.M., Wali, N., Sealy, I.M., White, R.J., Stemple, D.L., Collins, J.E., Busch-Nentwich, E.M. (2019) The gene regulatory basis of genetic compensation during neural crest induction. PLoS Genetics. 15:e1008213
- Liu, G., Wang, W., Hu, S., Wang, X., Zhang, Y. (2018) Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome research. 28(7):998-1007
- Ebrahimie, E., Moussavi-Nik, S.H., Newman, M., Van Der Hoek, M., Lardelli, M. (2016) The Zebrafish Equivalent of Alzheimer's Disease-Associated PRESENILIN Isoform PS2V Regulates Inflammatory and Other Responses to Hypoxic Stress. Journal of Alzheimer's disease : JAD. 52(2):581-608
- Xiao, C., Gao, L., Hou, Y., Xu, C., Chang, N., Wang, F., Hu, K., He, A., Luo, Y., Wang, J., Peng, J., Tang, F., Zhu, X., Xiong, J.W. (2016) Chromatin-remodelling factor Brg1 regulates myocardial proliferation and regeneration in zebrafish. Nature communications. 7:13787
- 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
1 - 10 of 30
Show