Gene
col4a4
- ID
- ZDB-GENE-101001-1
- Name
- collagen, type IV, alpha 4
- Symbol
- col4a4 Nomenclature History
- Previous Names
- None
- Type
- protein_coding_gene
- Location
- Chr: 15 Mapping Details/Browsers
- Description
- Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within glomerular basement membrane development and glomerular filtration. Predicted to be located in basement membrane and extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including gill; gonad primordium; hypodermis; lens; and pronephros. Used to study Alport syndrome. Human ortholog(s) of this gene implicated in autosomal recessive Alport syndrome; benign familial hematuria; and end stage renal disease. Orthologous to human COL4A4 (collagen type IV alpha 4 chain).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 6 figures from 5 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
- No data available
Wild Type Expression Summary
- All Phenotype Data
- 2 figures from Naylor et al., 2022
- Cross-Species Comparison
- Alliance
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| mn0275Gt | Transgenic insertion | Unknown | Unknown | DNA | |
| sa2802 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa6390 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa18383 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa22696 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa22697 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa32056 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa35965 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa42601 | Allele with one point mutation | Unknown | Premature Stop | ENU |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-col4a4 | Naylor et al., 2022 | |
| CRISPR2-col4a4 | Naylor et al., 2022 | |
| CRISPR3-col4a4 | Naylor et al., 2022 | |
| CRISPR4-col4a4 | Naylor et al., 2022 |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| autosomal recessive Alport syndrome | Alliance | Alport syndrome 2, autosomal recessive | 203780 |
| benign familial hematuria | Alliance | Hematuria, familial benign, 1 | 141200 |
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| Human Disease | Fish | Conditions | Citations |
|---|---|---|---|
| Alport syndrome | WT + CRISPR1-col4a4 + CRISPR2-col4a4 + CRISPR3-col4a4 + CRISPR4-col4a4 | standard conditions | Naylor et al., 2022 |
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Domain, Family, and Site Summary
Domain Details Per Protein
| Protein | Length | Collagen IV, non-collagenous | Collagen IV, non-collagenous domain superfamily | Collagen superfamily | Collagen triple helix repeat | C-type lectin fold |
|---|---|---|---|---|---|---|
|
UniProtKB:X1WFR7
|
1670 |
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| Type | Name | Annotation Method | Has Havana Data | Length (nt) | Analysis |
|---|---|---|---|---|---|
| mRNA |
col4a4-201
(1)
|
Ensembl | 10,607 nt | ||
| mRNA |
col4a4-202
(1)
|
Ensembl | 723 nt |
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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 | CH73-74H18 | ZFIN Curated Data | |
| Contained in | BAC | DKEY-29L4 | ZFIN Curated Data | |
| Contained in | BAC | DKEYP-110B2 | ZFIN Curated Data |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:XM_009291835 (1) | 9274 nt | ||
| Genomic | GenBank:BX571880 (2) | 194220 nt | ||
| Polypeptide | UniProtKB:X1WFR7 (1) | 1670 aa |
- LeBleu, V.S., Dai, J., Tsutakawa, S., MacDonald, B.A., Alge, J.L., Sund, M., Xie, L., Sugimoto, H., Tainer, J., Zon, L.I., Kalluri, R. (2023) Identification of unique α4 chain structure and conserved anti-angiogenic activity of α3NC1 type IV collagen in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 252(7):1046-1060
- Naylor, R.W., Lemarie, E., Jackson-Crawford, A., Davenport, J.B., Mironov, A., Lowe, M., Lennon, R. (2022) A novel nanoluciferase transgenic reporter measures proteinuria in zebrafish. Kidney International. 102(4):815-827
- Naylor, R.W., Watson, E., Williamson, S., Preston, R., Davenport, J.B., Thornton, N., Lowe, M., Williams, M., Lennon, R. (2022) Basement membrane defects in CD151-associated glomerular disease. Pediatric nephrology (Berlin, Germany). 37(12):3105-3115
- Blanc, M., Antczak, P., Cousin, X., Grunau, C., Scherbak, N., Rüegg, J., Keiter, S.H. (2021) The insecticide permethrin induces transgenerational behavioral changes linked to transcriptomic and epigenetic alterations in zebrafish (Danio rerio). The Science of the total environment. 779:146404
- Johnston, E.F., Cadonic, I.G., Craig, P.M., Gillis, T.E. (2019) microRNA-29b knocks down collagen type I production in cultured rainbow trout (Oncorhynchus mykiss) cardiac fibroblasts. The Journal of experimental biology. 222(Pt 17):
- Nicholas, C., Weaver, M., Piedade, W.P., Vocking, O., Famulski, J.K. (2019) Temporal characterization of optic fissure basement membrane composition suggests nidogen may be an initial target of remodeling. Developmental Biology. 452(1):43-54
- Xue, Y., Liu, D., Cui, G., Ding, Y., Ai, D., Gao, S., Zhang, Y., Suo, S., Wang, X., Lv, P., Zhou, C., Li, Y., Chen, X., Peng, G., Jing, N., Han, J.J., Liu, F. (2019) A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis. Cell Reports. 27:1567-1578.e5
- Bretaud, S., Nauroy, P., Malbouyres, M., Ruggiero, F. (2018) FISHING FOR COLLAGEN FUNCTION: ABOUT DEVELOPMENT, REGENERATION AND DISEASE. Seminars in cell & developmental biology. 89:100-108
- 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
- Westcot, S.E., Hatzold, J., Urban, M.D., Richetti, S.K., Skuster, K.J., Harm, R.M., Lopez Cervera, R., Umemoto, N., McNulty, M.S., Clark, K.J., Hammerschmidt, M., Ekker, S.C. (2015) Protein-Trap Insertional Mutagenesis Uncovers New Genes Involved in Zebrafish Skin Development, Including a Neuregulin 2a-Based ErbB Signaling Pathway Required during Median Fin Fold Morphogenesis. PLoS One. 10:e0130688
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