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Analysis of the cloned zebrafish β2 subunit gene and novel splice variants . Presentation and labeling as in Figure 1. A) Alignment of cloned human, rat, and zebrafish β2 amino acid sequences. Shown for zebrafish is the most conserved β2 splice form ( variant B ). S- = conserved cysteine in β2 that is a putative site of covalent linkage with a partner α subunit; S1 = nonsynonymous Hsβ2 single <t>nucleotide</t> polymorphism (SNP, C/T > R28W) (NCBI <t>dbSNP,</t> PharmGKB); S2 = nonsynonymous Hsβ2 SNP (G/A > R47H) (NCBI dbSNP, PharmGKB); GSCS = γ-secretase cleavage site. B) 5' and 3' RLM-RACE PCR and RT-PCR identified four distinct splice variants expressed from the zβ2 locus on zebrafish chromosome 15 ( Ensembl ). C) Splice donor and acceptor sites of zebrafish β2 splice variants. Zβ2 variants C and D both differ from the consensus sequences at the exon 4-intron 4 and intron 4-exon 5 splice junctions. D) Schematic diagram of β2 splice variants A-D. With the exception of variant A, the predicted proteins of zβ2 variants B-D differ only in the length of their intracytoplasmic C-terminal tail. Alignment of C-terminal tail of variants zβ2B, zβ2C, and zβ2D (below).
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Analysis of the cloned zebrafish β2 subunit gene and novel splice variants . Presentation and labeling as in Figure 1. A) Alignment of cloned human, rat, and zebrafish β2 amino acid sequences. Shown for zebrafish is the most conserved β2 splice form ( variant B ). S- = conserved cysteine in β2 that is a putative site of covalent linkage with a partner α subunit; S1 = nonsynonymous Hsβ2 single <t>nucleotide</t> polymorphism (SNP, C/T > R28W) (NCBI <t>dbSNP,</t> PharmGKB); S2 = nonsynonymous Hsβ2 SNP (G/A > R47H) (NCBI dbSNP, PharmGKB); GSCS = γ-secretase cleavage site. B) 5' and 3' RLM-RACE PCR and RT-PCR identified four distinct splice variants expressed from the zβ2 locus on zebrafish chromosome 15 ( Ensembl ). C) Splice donor and acceptor sites of zebrafish β2 splice variants. Zβ2 variants C and D both differ from the consensus sequences at the exon 4-intron 4 and intron 4-exon 5 splice junctions. D) Schematic diagram of β2 splice variants A-D. With the exception of variant A, the predicted proteins of zβ2 variants B-D differ only in the length of their intracytoplasmic C-terminal tail. Alignment of C-terminal tail of variants zβ2B, zβ2C, and zβ2D (below).
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Analysis of the cloned zebrafish β2 subunit gene and novel splice variants . Presentation and labeling as in Figure 1. A) Alignment of cloned human, rat, and zebrafish β2 amino acid sequences. Shown for zebrafish is the most conserved β2 splice form ( variant B ). S- = conserved cysteine in β2 that is a putative site of covalent linkage with a partner α subunit; S1 = nonsynonymous Hsβ2 single <t>nucleotide</t> polymorphism (SNP, C/T > R28W) (NCBI <t>dbSNP,</t> PharmGKB); S2 = nonsynonymous Hsβ2 SNP (G/A > R47H) (NCBI dbSNP, PharmGKB); GSCS = γ-secretase cleavage site. B) 5' and 3' RLM-RACE PCR and RT-PCR identified four distinct splice variants expressed from the zβ2 locus on zebrafish chromosome 15 ( Ensembl ). C) Splice donor and acceptor sites of zebrafish β2 splice variants. Zβ2 variants C and D both differ from the consensus sequences at the exon 4-intron 4 and intron 4-exon 5 splice junctions. D) Schematic diagram of β2 splice variants A-D. With the exception of variant A, the predicted proteins of zβ2 variants B-D differ only in the length of their intracytoplasmic C-terminal tail. Alignment of C-terminal tail of variants zβ2B, zβ2C, and zβ2D (below).
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Analysis of the cloned zebrafish β2 subunit gene and novel splice variants . Presentation and labeling as in Figure 1. A) Alignment of cloned human, rat, and zebrafish β2 amino acid sequences. Shown for zebrafish is the most conserved β2 splice form ( variant B ). S- = conserved cysteine in β2 that is a putative site of covalent linkage with a partner α subunit; S1 = nonsynonymous Hsβ2 single <t>nucleotide</t> polymorphism (SNP, C/T > R28W) (NCBI <t>dbSNP,</t> PharmGKB); S2 = nonsynonymous Hsβ2 SNP (G/A > R47H) (NCBI dbSNP, PharmGKB); GSCS = γ-secretase cleavage site. B) 5' and 3' RLM-RACE PCR and RT-PCR identified four distinct splice variants expressed from the zβ2 locus on zebrafish chromosome 15 ( Ensembl ). C) Splice donor and acceptor sites of zebrafish β2 splice variants. Zβ2 variants C and D both differ from the consensus sequences at the exon 4-intron 4 and intron 4-exon 5 splice junctions. D) Schematic diagram of β2 splice variants A-D. With the exception of variant A, the predicted proteins of zβ2 variants B-D differ only in the length of their intracytoplasmic C-terminal tail. Alignment of C-terminal tail of variants zβ2B, zβ2C, and zβ2D (below).
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Analysis of the cloned zebrafish β2 subunit gene and novel splice variants . Presentation and labeling as in Figure 1. A) Alignment of cloned human, rat, and zebrafish β2 amino acid sequences. Shown for zebrafish is the most conserved β2 splice form ( variant B ). S- = conserved cysteine in β2 that is a putative site of covalent linkage with a partner α subunit; S1 = nonsynonymous Hsβ2 single <t>nucleotide</t> polymorphism (SNP, C/T > R28W) (NCBI <t>dbSNP,</t> PharmGKB); S2 = nonsynonymous Hsβ2 SNP (G/A > R47H) (NCBI dbSNP, PharmGKB); GSCS = γ-secretase cleavage site. B) 5' and 3' RLM-RACE PCR and RT-PCR identified four distinct splice variants expressed from the zβ2 locus on zebrafish chromosome 15 ( Ensembl ). C) Splice donor and acceptor sites of zebrafish β2 splice variants. Zβ2 variants C and D both differ from the consensus sequences at the exon 4-intron 4 and intron 4-exon 5 splice junctions. D) Schematic diagram of β2 splice variants A-D. With the exception of variant A, the predicted proteins of zβ2 variants B-D differ only in the length of their intracytoplasmic C-terminal tail. Alignment of C-terminal tail of variants zβ2B, zβ2C, and zβ2D (below).
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Image Search Results


Analysis of the cloned zebrafish β2 subunit gene and novel splice variants . Presentation and labeling as in Figure 1. A) Alignment of cloned human, rat, and zebrafish β2 amino acid sequences. Shown for zebrafish is the most conserved β2 splice form ( variant B ). S- = conserved cysteine in β2 that is a putative site of covalent linkage with a partner α subunit; S1 = nonsynonymous Hsβ2 single nucleotide polymorphism (SNP, C/T > R28W) (NCBI dbSNP, PharmGKB); S2 = nonsynonymous Hsβ2 SNP (G/A > R47H) (NCBI dbSNP, PharmGKB); GSCS = γ-secretase cleavage site. B) 5' and 3' RLM-RACE PCR and RT-PCR identified four distinct splice variants expressed from the zβ2 locus on zebrafish chromosome 15 ( Ensembl ). C) Splice donor and acceptor sites of zebrafish β2 splice variants. Zβ2 variants C and D both differ from the consensus sequences at the exon 4-intron 4 and intron 4-exon 5 splice junctions. D) Schematic diagram of β2 splice variants A-D. With the exception of variant A, the predicted proteins of zβ2 variants B-D differ only in the length of their intracytoplasmic C-terminal tail. Alignment of C-terminal tail of variants zβ2B, zβ2C, and zβ2D (below).

Journal: BMC Evolutionary Biology

Article Title: Molecular cloning and analysis of zebrafish voltage-gated sodium channel beta subunit genes: implications for the evolution of electrical signaling in vertebrates

doi: 10.1186/1471-2148-7-113

Figure Lengend Snippet: Analysis of the cloned zebrafish β2 subunit gene and novel splice variants . Presentation and labeling as in Figure 1. A) Alignment of cloned human, rat, and zebrafish β2 amino acid sequences. Shown for zebrafish is the most conserved β2 splice form ( variant B ). S- = conserved cysteine in β2 that is a putative site of covalent linkage with a partner α subunit; S1 = nonsynonymous Hsβ2 single nucleotide polymorphism (SNP, C/T > R28W) (NCBI dbSNP, PharmGKB); S2 = nonsynonymous Hsβ2 SNP (G/A > R47H) (NCBI dbSNP, PharmGKB); GSCS = γ-secretase cleavage site. B) 5' and 3' RLM-RACE PCR and RT-PCR identified four distinct splice variants expressed from the zβ2 locus on zebrafish chromosome 15 ( Ensembl ). C) Splice donor and acceptor sites of zebrafish β2 splice variants. Zβ2 variants C and D both differ from the consensus sequences at the exon 4-intron 4 and intron 4-exon 5 splice junctions. D) Schematic diagram of β2 splice variants A-D. With the exception of variant A, the predicted proteins of zβ2 variants B-D differ only in the length of their intracytoplasmic C-terminal tail. Alignment of C-terminal tail of variants zβ2B, zβ2C, and zβ2D (below).

Article Snippet: BLAST Basic local alignment search tool BLASTN BLAST nucleotide BLASTP BLAST protein dbSNP Database of single nucleotide polymorphisms HUGO Human genome organization IRES Internal ribosomal entry site mRNA Message ribonucleic acid Na v 1 Voltage-gated sodium channel, family 1 NCBI National Center for Biotechnology Information Para Paralytic gene, Drosophila PCR Polymerase chain reaction PharmGKB Pharmacogenomics knowledge base RACE Rapid amplification of cDNA ends RT-PCR Reverse transcription polymerase chain reaction SNPs Single nucleotide polymorphisms TEH1-4Tip-E homologous genes 1–4 Tip-ETemperature-induced paralysis gene, Drosophila TMPred Transmembrane prediction software UTR Untranslated region zβ1 zebrafish sodium channel beta 1 subunit gene (zebrafish scn1b ). zβ2 zebrafish sodium channel beta 2 subunit gene (zebrafish scn2b ). zβ3 zebrafish sodium channel beta 3 subunit gene (zebrafish scn3b ). zβ4.1 zebrafish sodium channel beta 4.1 subunit gene (zebrafish scn4.1b ). zβ4.2 zebrafish sodium channel beta 4.2 subunit gene (zebrafish scn4.2b ). z scn5a zebrafish homolog to the mammalian sodium channel pore-forming α subunit gene scn5a .

Techniques: Clone Assay, Labeling, Variant Assay, Reverse Transcription Polymerase Chain Reaction