Gene
sf3b4
- ID
- ZDB-GENE-020419-22
- Name
- splicing factor 3b, subunit 4
- Symbol
- sf3b4 Nomenclature History
- Previous Names
-
- chunp6902
- fb36a04
- wu:fb36a04 (1)
- Type
- protein_coding_gene
- Location
- Chr: 19 Mapping Details/Browsers
- Description
- Predicted to enable RNA binding activity. Acts upstream of or within regulation of retina development in camera-type eye and visual behavior. Predicted to be located in nucleus. Predicted to be part of U2 snRNP and precatalytic spliceosome. Is expressed in head. Human ortholog(s) of this gene implicated in Nager acrofacial dysostosis; cervical cancer; and hepatocellular carcinoma. Orthologous to human SF3B4 (splicing factor 3b subunit 4).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 3 figures from 3 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
-
- MGC:85842 (1 image)
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 |
|---|---|---|---|---|---|
| hi1159Tg | Transgenic insertion | Intron 1 | Unknown | DNA | |
| hi4070Tg | Transgenic insertion | Intron 1 | Unknown | DNA | |
| la020945Tg | Transgenic insertion | Unknown | Unknown | DNA | |
| la020946Tg | Transgenic insertion | Unknown | Unknown | DNA |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-sf3b4 | Parvez et al., 2021 | |
| CRISPR2-sf3b4 | Parvez et al., 2021 | |
| CRISPR3-sf3b4 | Parvez et al., 2021 | |
| CRISPR4-sf3b4 | Parvez et al., 2021 |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| Nager acrofacial dysostosis | Alliance | Acrofacial dysostosis 1, Nager type | 154400 |
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Domain, Family, and Site Summary
| Type | InterPro ID | Name |
|---|---|---|
| Domain | IPR000504 | RNA recognition motif domain |
| Domain | IPR034158 | SF3B4, RNA recognition motif 1 |
| Domain | IPR034159 | SF3B4, RNA recognition motif 2 |
| Family | IPR052084 | Spliceosome-associated SF3B4 subunit |
| Homologous_superfamily | IPR012677 | Nucleotide-binding alpha-beta plait domain superfamily |
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Domain Details Per Protein
| Protein | Additional Resources | Length | Nucleotide-binding alpha-beta plait domain superfamily | RNA-binding domain superfamily | RNA recognition motif domain | SF3B4, RNA recognition motif 1 | SF3B4, RNA recognition motif 2 | Spliceosome-associated SF3B4 subunit |
|---|---|---|---|---|---|---|---|---|
| UniProtKB:Q6NWB3 | InterPro | 400 |
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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 | CH73-312O15 | ZFIN Curated Data | |
| Contained in | BAC | CH211-210H11 | ZFIN Curated Data | |
| Contained in | BAC | DKEYP-84F11 | ZFIN Curated Data | |
| Encodes | EST | fb36a04 | ZFIN Curated Data | |
| Encodes | STS | chunp6902 | ||
| Encodes | cDNA | MGC:65961 | ZFIN Curated Data | |
| Encodes | cDNA | MGC:85842 | ZFIN Curated Data |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:NM_153661 (1) | 1395 nt | ||
| Genomic | GenBank:BX890617 (1) | 182182 nt | ||
| Polypeptide | UniProtKB:Q6NWB3 (1) | 400 aa |
- Ulhaq, Z.S., Ogino, Y., Tse, W.K.F. (2024) Transcriptome alterations in sf3b4-depleted zebrafish: Insights into cataract formation in retinitis pigmentosa model. Experimental Eye Research. 240:109819
- Ulhaq, Z.S., Tse, W.K.F. (2024) Transcriptomic analysis reveals mitochondrial dysfunction in the pathogenesis of Nager syndrome in sf3b4-depleted zebrafish. Biochimica et biophysica acta. Molecular basis of disease. 1870(4):167128
- Ulhaq, Z.S., Okamoto, K., Ogino, Y., Fai Tse, W.K. (2023) Dysregulation of spliceosomes complex induces retinitis pigmentosa-like characteristics in sf3b4-depleted zebrafish. The American journal of pathology. 193(9):1223-1233
- Parvez, S., Herdman, C., Beerens, M., Chakraborti, K., Harmer, Z.P., Yeh, J.J., MacRae, C.A., Yost, H.J., Peterson, R.T. (2021) MIC-Drop: A platform for large-scale in vivo CRISPR screens. Science (New York, N.Y.). 373(6559):1146-1151
- Xu, H., Wang, G., Chi, Y.Y., Kou, Y.X., Li, Y. (2021) Expression profiling and functional characterization of the duplicated Oxr1b gene in zebrafish. Comparative biochemistry and physiology. Part D, Genomics & proteomics. 39:100857
- Lee, Y.R., Khan, K., Armfield-Uhas, K., Srikanth, S., Thompson, N.A., Pardo, M., Yu, L., Norris, J.W., Peng, Y., Gripp, K.W., Aleck, K.A., Li, C., Spence, E., Choi, T.I., Kwon, S.J., Park, H.M., Yu, D., Do Heo, W., Mooney, M.R., Baig, S.M., Wentzensen, I.M., Telegrafi, A., McWalter, K., Moreland, T., Roadhouse, C., Ramsey, K., Lyons, M.J., Skinner, C., Alexov, E., Katsanis, N., Stevenson, R.E., Choudhary, J.S., Adams, D.J., Kim, C.H., Davis, E.E., Schwartz, C.E. (2020) Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy. Nature communications. 11:3698
- 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
- Varshney, G.K., Lu, J., Gildea, D., Huang, H., Pei, W., Yang, Z., Huang, S.C., Schoenfeld, D.S., Pho, N., Casero, D., Hirase, T., Mosbrook-Davis, D.M., Zhang, S., Jao, L.E., Zhang, B., Woods, I.G., Zimmerman, S., Schier, A.F., Wolfsberg, T., Pellegrini, M., Burgess, S.M., and Lin, S. (2013) A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome research. 23(4):727-735
- Wang, D., Jao, L.E., Zheng, N., Dolan, K., Ivey, J., Zonies, S., Wu, X., Wu, K., Yang, H., Meng, Q., Zhu, Z., Zhang, B., Lin, S., and Burgess, S.M. (2007) Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proceedings of the National Academy of Sciences of the United States of America. 104(30):12428-12433
- Amsterdam, A., Nissen, R.M., Sun, Z., Swindell, E., Farrington, S., and Hopkins, N. (2004) Identification of 315 genes essential for early zebrafish development. Proceedings of the National Academy of Sciences of the United States of America. 101(35):12792-12797
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