Gene
nid2a
- ID
- ZDB-GENE-030827-2
- Name
- nidogen 2a (osteonidogen)
- Symbol
- nid2a Nomenclature History
- Previous Names
-
- nid2
- chunp382
- fb77a09
- fc18d04
- im:7144424
- wu:fb77a09
- wu:fc18d04
- Type
- protein_coding_gene
- Location
- Chr: 17 Mapping Details/Browsers
- Description
- Predicted to enable calcium ion binding activity. Acts upstream of or within closure of optic fissure and fin regeneration. Predicted to be located in extracellular region. Predicted to be active in basement membrane and extracellular space. Is expressed in several structures, including axis; digestive system; head mesenchyme; nervous system; and pectoral fin bud. Orthologous to human NID2 (nidogen 2).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 18 figures from 7 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
-
- IMAGE:7144424 (21 images)
Wild Type Expression Summary
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| sa15802 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa23022 | Allele with one point mutation | Unknown | Splice Site | ENU | |
| sa25037 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa36357 | Allele with one point mutation | Unknown | Unknown | ENU | |
| sa44869 | Allele with one point mutation | Unknown | Unknown | ENU | |
| zju105Tg | Transgenic insertion | Unknown | Unknown | DNA | |
| zju114 | Allele with one delins | Unknown | Unknown | CRISPR |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-nid2a | Varshney et al., 2015 | |
| CRISPR2-nid2a | Varshney et al., 2015 | |
| CRISPR3-nid2a | Ma et al., 2017 | |
| MO1-nid2a | N/A | (2) |
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Human Disease
Domain, Family, and Site Summary
| Type | InterPro ID | Name |
|---|---|---|
| Conserved_site | IPR018097 | EGF-like calcium-binding, conserved site |
| Domain | IPR000716 | Thyroglobulin type-1 |
| Domain | IPR000742 | EGF-like domain |
| Domain | IPR001881 | EGF-like calcium-binding domain |
| Domain | IPR003886 | NIDO domain |
| Domain | IPR006605 | G2 nidogen/fibulin G2F |
| Domain | IPR024731 | EGF domain |
| Domain | IPR049883 | NOTCH1 EGF-like calcium-binding domain |
| Family | IPR051950 | Developmental regulator and protease inhibitor |
| Homologous_superfamily | IPR009017 | Green fluorescent protein |
| Homologous_superfamily | IPR009030 | Growth factor receptor cysteine-rich domain superfamily |
| Homologous_superfamily | IPR011042 | Six-bladed beta-propeller, TolB-like |
| Homologous_superfamily | IPR036857 | Thyroglobulin type-1 superfamily |
| PTM | IPR000152 | EGF-type aspartate/asparagine hydroxylation site |
| Repeat | IPR000033 | LDLR class B repeat |
Domain Details Per Protein
| Protein | Additional Resources | Length | Developmental regulator and protease inhibitor | EGF domain | EGF-like calcium-binding, conserved site | EGF-like calcium-binding domain | EGF-like domain | EGF-type aspartate/asparagine hydroxylation site | G2 nidogen/fibulin G2F | Green fluorescent protein | Growth factor receptor cysteine-rich domain superfamily | LDLR class B repeat | NIDO domain | NOTCH1 EGF-like calcium-binding domain | Six-bladed beta-propeller, TolB-like | Thyroglobulin type-1 | Thyroglobulin type-1 superfamily |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| UniProtKB:A0A8M2BH70 | InterPro | 1804 | |||||||||||||||
| UniProtKB:A0A8M2BH21 | InterPro | 1576 | |||||||||||||||
| UniProtKB:A0A8M2BH48 | InterPro | 1424 | |||||||||||||||
| UniProtKB:A0A8M2BH51 | InterPro | 1728 | |||||||||||||||
| UniProtKB:A0A8M9PEL7 | InterPro | 1728 | |||||||||||||||
| UniProtKB:A0A8M2BHK2 | InterPro | 1652 | |||||||||||||||
| UniProtKB:A0A8M6YTZ1 | InterPro | 1576 |
| Type | Name | Annotation Method | Has Havana Data | Length (nt) | Analysis |
|---|---|---|---|---|---|
| mRNA |
nid2a-201
(1)
|
Ensembl | 773 nt | ||
| mRNA |
nid2a-202
(1)
|
Ensembl | 5,230 nt | ||
| mRNA |
nid2a-203
(1)
|
Ensembl | 814 nt | ||
| mRNA |
nid2a-204
(1)
|
Ensembl | 649 nt | ||
| mRNA |
nid2a-205
(1)
|
Ensembl | 423 nt | ||
| mRNA |
nid2a-206
(1)
|
Ensembl | 838 nt | ||
| mRNA |
nid2a-207
(1)
|
Ensembl | 728 nt |
Interactions and Pathways
No data available
Plasmids
No data available
No data available
| Relationship | Marker Type | Marker | Accession Numbers | Citations |
|---|---|---|---|---|
| Contained in | BAC | CH73-32L23 | ZFIN Curated Data | |
| Contained in | BAC | CH211-266O15 | ZFIN Curated Data | |
| Encodes | EST | fb77a09 | ||
| Encodes | EST | fc18d04 | ||
| Encodes | EST | IMAGE:7144424 | Thisse et al., 2004 | |
| Has Artifact | EST | fc87b12 |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:XM_005169847 (1) | 5898 nt | ||
| Genomic | GenBank:CR387921 (1) | 187568 nt | ||
| Polypeptide | UniProtKB:A0A8M2BH70 (1) | 1804 aa |
- Comparative Orthology
- Alliance
- Kolb, J., Tsata, V., John, N., Kim, K., Möckel, C., Rosso, G., Kurbel, V., Parmar, A., Sharma, G., Karandasheva, K., Abuhattum, S., Lyraki, O., Beck, T., Müller, P., Schlüßler, R., Frischknecht, R., Wehner, A., Krombholz, N., Steigenberger, B., Beis, D., Takeoka, A., Blümcke, I., Möllmert, S., Singh, K., Guck, J., Kobow, K., Wehner, D. (2023) Small leucine-rich proteoglycans inhibit CNS regeneration by modifying the structural and mechanical properties of the lesion environment. Nature communications. 14:68146814
- Bryan, C.D., Casey, M.A., Pfeiffer, R.L., Jones, B.W., Kwan, K.M. (2020) Optic cup morphogenesis requires neural crest-mediated basement membrane assembly. Development (Cambridge, England). 147(4):
- Ma, Z., Zhu, P., Shi, H., Guo, L., Zhang, Q., Chen, Y., Chen, S., Zhang, Z., Peng, J., Chen, J. (2019) PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature. 568(7751):259-263
- 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
- Ma, Z., Zhu, P., Pang, M., Guo, L., Chang, N., Zheng, J., Zhu, X., Gao, C., Huang, H., Cui, Z., Xiong, J.W., Peng, J., Chen, J. (2017) A novel inducible mutagenesis screen enables to isolate and clone both embryonic and adult zebrafish mutants. Scientific Reports. 7:10381
- Zhu, P., Ma, Z., Guo, L., Zhang, W., Zhang, Q., Zhao, T., Jiang, K., Peng, J., Chen, J. (2017) Short body length phenotype is compensated by the upregulation of nidogen family members in a deleterious nid1a mutation of zebrafish. Journal of genetics and genomics = Yi chuan xue bao. 44(11):553-556
- Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48(4):427-37
- 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
- Kessels, M.Y., Huitema, L.F., Boeren, S., Kranenbarg, S., Schulte-Merker, S., van Leeuwen, J.L., de Vries, S.C. (2014) Proteomics analysis of the zebrafish skeletal extracellular matrix. PLoS One. 9:e90568
- Yoda, H., Momoi, A., Esguerra, C.V., Meyer, D., Driever, W., Kondoh, H., and Furutani-Seiki, M. (2003) An expression pattern screen for genes involved in the induction of the posterior nervous system of zebrafish. Differentiation; research in biological diversity. 71(2):152-162
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