Gene
pcdh15b
- ID
- ZDB-GENE-050214-1
- Name
- protocadherin-related 15b
- Symbol
- pcdh15b Nomenclature History
- Previous Names
-
- im:7151077
- si:ch211-253p2.2
- Type
- protein_coding_gene
- Location
- Chr: 12 Mapping Details/Browsers
- Description
- Predicted to have calcium ion binding activity. Involved in detection of light stimulus involved in visual perception and eye development. Predicted to localize to integral component of plasma membrane. Human ortholog(s) of this gene implicated in Usher syndrome type 1D; Usher syndrome type 1F; and autosomal recessive nonsyndromic deafness 23. Is expressed in brain; epiphysis; eye; and retinal photoreceptor layer. Orthologous to human PCDH15 (protocadherin related 15).
- Genome Resources
- Note
- None
- Comparative Information
- All Expression Data
- 3 figures from 2 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
- No data available
Wild Type Expression Summary
- All Phenotype Data
- No data available
- Cross-Species Comparison
- Alliance
Phenotype Summary
Mutations
Allele | Type | Localization | Consequence | Mutagen | Supplier |
---|---|---|---|---|---|
la018346Tg | Transgenic insertion | Unknown | Unknown | DNA | |
la018347Tg | Transgenic insertion | Unknown | Unknown | DNA | |
sa22026 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
sa22027 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
sa27884 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
sa30955 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
sa35208 | Allele with one point mutation | Unknown | Splice Site | ENU | |
sa45449 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
uot14 | Allele with one deletion | Unknown | Unknown | CRISPR | |
uot15 | Allele with one insertion | Unknown | Unknown | CRISPR |
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Targeting Reagent | Created Alleles | Citations |
---|---|---|
CRISPR1-pcdh15b | Varshney et al., 2015 | |
CRISPR2-pcdh15b | (2) | |
CRISPR3-pcdh15b | (4) | |
MO1-pcdh15b | N/A | Seiler et al., 2005 |
MO2-pcdh15b | N/A | Seiler et al., 2005 |
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Human Disease
Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
---|---|---|---|
autosomal recessive nonsyndromic deafness 23 | Alliance | Deafness, autosomal recessive 23 | 609533 |
Usher syndrome type 1D | Alliance | Usher syndrome, type 1D/F digenic | 601067 |
Usher syndrome type 1F | Alliance | Usher syndrome, type 1F | 602083 |
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Human Disease | Fish | Conditions | Citations |
---|---|---|---|
Usher syndrome type 1F | pcdh15buot14/uot14 | standard conditions | Miles et al., 2021 |
Usher syndrome type 1F | pcdh15buot15/uot15 | standard conditions | Miles et al., 2021 |
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Domain, Family, and Site Summary
Domain Details Per Protein
Protein | Length | Cadherin | Cadherin conserved site | Cadherin-like | Cadherin-like superfamily | Extracellular cadherin domain | Extracellular cadherin domain superfamily |
---|---|---|---|---|---|---|---|
UniProtKB:A0A8M3B4E7
|
1951 | ||||||
UniProtKB:Q5ICW5
|
1907 | ||||||
UniProtKB:A0A8M3B781
|
1959 | ||||||
UniProtKB:A0A8M3AY44
|
1727 | ||||||
UniProtKB:A0A8M3AY16
|
1964 |
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Type | Name | Annotation Method | Has Havana Data | Length (nt) | Analysis |
---|---|---|---|---|---|
mRNA |
pcdh15b-201
(1)
|
Ensembl | 5,636 nt | ||
mRNA |
pcdh15b-202
(1)
|
Ensembl | 324 nt | ||
mRNA |
si:ch211-253p2.2-201
(1)
|
Ensembl | 2,794 nt |
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Interactions and Pathways
No data available
Name | Type | Antigen Genes | Isotype | Host Organism | Assay | Source | Citations |
---|---|---|---|---|---|---|---|
Ab1-pcdh15 |
|
NSJ Bioreagents
|
2 |
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Plasmids
No data available
No data available
Relationship | Marker Type | Marker | Accession Numbers | Citations |
---|---|---|---|---|
Contained in | BAC | CH73-210E1 | ZFIN Curated Data | |
Contained in | BAC | CH73-277C13 | ZFIN Curated Data | |
Contained in | BAC | CH211-117C16 | ZFIN Curated Data | |
Contained in | BAC | CH211-200L21 | ZFIN Curated Data | |
Contained in | BAC | CH211-253P2 | ZFIN Curated Data | |
Contained in | BAC | DKEY-93D9 | ZFIN Curated Data | |
Encodes | EST | IMAGE:7151077 | Thisse et al., 2004 |
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Type | Accession # | Sequence | Length (nt/aa) | Analysis |
---|---|---|---|---|
RNA | RefSeq:NM_001012486 (1) | 6059 nt | ||
Genomic | GenBank:CR925795 (1) | 212255 nt | ||
Polypeptide | UniProtKB:A0A8M3AY16 (1) | 1964 aa |
Species | Symbol | Chromosome | Accession # | Evidence |
---|---|---|---|---|
Human | PCDH15 | 10 | Amino acid sequence comparison (1) |
- Miles, A., Blair, C., Emili, A., Tropepe, V. (2021) Usher syndrome Type 1-associated gene, pcdh15b, is required for photoreceptor structural integrity in zebrafish. Disease models & mechanisms. 14(12):
- 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
- Varshney, G.K., Pei, W., LaFave, M.C., Idol, J., Xu, L., Gallardo, V., Carrington, B., Bishop, K., Jones, M., Li, M., Harper, U., Huang, S.C., Prakash, A., Chen, W., Sood, R., Ledin, J., Burgess, S.M. (2015) High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome research. 25(7):1030-42
- Rey, S., Boltana, S., Vargas, R., Roher, N., and Mackenzie, S. (2013) Combining animal personalities with transcriptomics resolves individual variation within a wild-type zebrafish population and identifies underpinning molecular differences in brain function. Molecular Ecology. 22(24):6100-15
- 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
- Seiler, C., Finger-Baier, K.C., Rinner, O., Makhankov, Y.V., Schwarz, H., Neuhauss, S.C., and Nicolson, T. (2005) Duplicated genes with split functions: independent roles of protocadherin15 orthologues in zebrafish hearing and vision. Development (Cambridge, England). 132(3):615-623
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