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Open Access Research article

A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes - an open access resource for neuroscience and evolutionary biology

Molly Craxton

Author Affiliations

Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK

BMC Genomics 2010, 11:37  doi:10.1186/1471-2164-11-37

Published: 15 January 2010

Additional files

Additional file 1:

Comprehensive information about the marine invertebrate genes in this collection. This spreadsheet file (MarineInvertebrates.xls) contains full details of each gene identified in the marine invertebrate genomes in this collection.

Format: XLS Size: 666KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Comprehensive information about the ecdysozoan genes in this collection. This spreadsheet file (Ecdysozoa.xls) contains full details of each gene identified in the ecdysozoan genomes in this collection.

Format: XLS Size: 1.4MB Download file

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Open Data

Additional file 3:

Comprehensive information about the vertebrate genes in this collection. This spreadsheet file (Vertebrates.xls) contains full details of each gene identified in the vertebrate genomes in this collection.

Format: XLS Size: 2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Comprehensive information about the SNARE and complexin genes identified in T. adhaerens and N. vectensis. This spreadsheet file (SNAREs.xls) contains full details of the genes identified in T. adhaerens and N. vectensis which are similar to neuronal SNAREs and complexin.

Format: XLS Size: 48KB Download file

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Open Data

Additional file 5:

Dendrogram of relationships among the invertebrate sequences in this collection. Additional file 5 displays the guide tree of the clustalw2 comparison of the invertebrate sequences in this collection, excluding variants, totalling 356 sequences. Genes which encode mutually exclusive alternative exons are highlighted with a green box. Conserved groups of Syt genes which have not previously been described, are highlighted with a blue box.

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Open Data

Additional file 6:

Dendrogram of relationships among the vertebrate sequences in this collection. Additional file 6 displays the guide tree of the clustalw2 comparison of the vertebrate sequences in this collection, excluding variants, totalling 355 sequences. Mouse genes are highlighted with a red box. Conserved groups of Syt genes which have not previously been described, are highlighted with a blue box.

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Open Data

Additional file 7:

Dendrogram of relationships among the invertebrate and mammalian sequences in this collection. Additional file 7 displays the guide tree of the clustalw2 comparison of the invertebrate sequences (one representative per genus) excluding variants, plus mammalian sequences, excluding variants, totalling 289 sequences. Mouse genes are highlighted with a red box. Conserved groups of Syt genes which have not previously been described, are highlighted with a blue box.

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Open Data

Additional file 8:

Dendrogram of relationships among the invertebrate and vertebrate sequences in this collection. Additional file 8 displays the guide tree of the clustalw2 comparison of the invertebrate sequences (one representative per genus) excluding variants, plus a subset of vertebrate sequences, excluding variants, totalling 454 sequences. Mouse genes are highlighted with a red box. Conserved groups of Syt genes which have not previously been described, are highlighted with a blue box.

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Open Data

Additional file 9:

Alignment of the invertebrate Syt1 sequences, plus Caenorhabditis snt-3. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

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Open Data

Additional file 10:

Alignment of the vertebrate Syt1 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. Conserved N-glycosylation consensus sites are indicated by blue boxes. The conserved threonine, which can be O-glycosylated is also indicated by a blue box. X residues indicate where a portion of sequence is missing.

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Open Data

Additional file 11:

Alignment of the vertebrate Syt2 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. The X. tropicalis splice variant is included and highlighted with a black dot where it differs. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 92KB Download file

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Open Data

Additional file 12:

Alignment of the vertebrate Syt5 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 134KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 13:

Alignment of the vertebrate Syt8 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 90KB Download file

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Open Data

Additional file 14:

Alignment of the invertebrate Syt4 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 181KB Download file

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Open Data

Additional file 15:

Alignment of the vertebrate Syt4 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. The G. gallus splice variant is included and highlighted with a black dot where it differs. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 85KB Download file

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Open Data

Additional file 16:

Alignment of the vertebrate Syt11 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 89KB Download file

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Open Data

Additional file 17:

Alignment of the invertebrate Syt7 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. The D. melanogaster splice variant is included and highlighted with a black dot where it differs. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 205KB Download file

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Open Data

Additional file 18:

Alignment of the vertebrate Syt7 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 233KB Download file

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Open Data

Additional file 19:

Alignment of the invertebrate Syt9 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 44KB Download file

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Open Data

Additional file 20:

Alignment of the vertebrate Syt9 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 149KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 21:

Alignment of the vertebrate Syt3 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 79KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 22:

Alignment of the vertebrate Syt6 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 183KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 23:

Alignment of the vertebrate Syt10 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment.

Format: PDF Size: 87KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 24:

Alignment of the invertebrate Syt12 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. Because of their differing positions, TM domains are highlighted in blue. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 209KB Download file

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Open Data

Additional file 25:

Alignment of the vertebrate Syt12 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. The H. sapiens splice variant is included and highlighted with a black dot where it differs. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 84KB Download file

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Open Data

Additional file 26:

Alignment of the invertebrate Syt13 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants which specify an alternative N-terminus lacking a TM domain, are indicated on top, with a dotted line indicating where they join the common C-terminal portion. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, upstream of the C2A domain, is indicated. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 156KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 27:

Alignment of the vertebrate Syt13 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. The H. sapiens splice variant is included and highlighted with a black dot where it differs. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 72KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 28:

Alignment of the invertebrate Syt15 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. Because of their differing positions, TM domains are highlighted in blue. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 87KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 29:

Alignment of the vertebrate Syt15 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 137KB Download file

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Open Data

Additional file 30:

Alignment of the invertebrate Syt16 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants which specify alternative N-termini lacking TM domains, are included and highlighted with black dots where their sequences differ. TM domains are highlighted in blue. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 215KB Download file

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Open Data

Additional file 31:

Alignment of the vertebrate Syt16 sequences which have TM domains. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 96KB Download file

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Open Data

Additional file 32:

Alignment of the vertebrate Syt16 sequences which lack TM domains. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 127KB Download file

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Open Data

Additional file 33:

Alignment of the vertebrate Syt14 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 286KB Download file

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Open Data

Additional file 34:

Alignment of the invertebrate Syt17 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, upstream of the C2A domain, is indicated. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 36KB Download file

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Open Data

Additional file 35:

Alignment of the vertebrate Syt17 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. A possible motif just upstream of the C2A domain, is indicated. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 122KB Download file

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Open Data

Additional file 36:

Alignment of the invertebrate Sytalpha sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The widely conserved motif of unknown function, just upstream of the C2A domain, is indicated. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 148KB Download file

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Open Data

Additional file 37:

Alignment of the Syt18 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

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Open Data

Additional file 38:

Alignment of the vertebrate Syt19 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. The X residue indicates where a portion of sequence is missing.

Format: PDF Size: 42KB Download file

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Open Data

Additional file 39:

Alignment of the invertebrate Syt21 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. TM sequences are highlighted in blue. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 47KB Download file

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Open Data

Additional file 40:

Alignment of the N. vectensis Syt sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. TM sequences are highlighted in blue. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 142KB Download file

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Open Data

Additional file 41:

Alignment of the invertebrate Dblc2 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns.

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Open Data

Additional file 42:

Alignment of the invertebrate Esyt2 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. X residues indicate where a portion of sequence is missing.

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Open Data

Additional file 43:

Alignment of the mutually exclusive alternative Esyt2 exons. In addition to the alternatively coded exon which is highlighted, the exon upstream and the exon downstream are shown. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Blue bars indicate phase +2 introns.

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Open Data

Additional file 44:

Alignment of the vertebrate Esyt1 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. The middle portion is only present in the fish esyt1b sequences. A pink dot in this portion, marks an intron loss in T. rubripes and T. nigroviridis. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Blue bars indicate phase +2 introns. X residues indicate where a portion of sequence is missing.

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Open Data

Additional file 45:

Alignment of the vertebrate Esyt2 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Blue bars indicate phase +2 introns. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 287KB Download file

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Open Data

Additional file 46:

Alignment of the vertebrate Esyt3 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. Some intron positions are marked with dotted lines. In these cases, transcript sequence covers a gap in the genomic sequence and the intron presence is assumed. X residues indicate where a portion of sequence is missing.

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Open Data

Additional file 47:

Alignment of the invertebrate Rabphilin sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are indicated. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The five conserved acidic amino acids in each C2 domain are indicated by pink dots at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 396KB Download file

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Open Data

Additional file 48:

Alignment of the vertebrate Rabphilin (Rph3a) sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 159KB Download file

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Open Data

Additional file 49:

Alignment of the vertebrate Rph3al sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. X residues indicate where a portion of sequence is missing.

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Open Data

Additional file 50:

Alignment of the vertebrate Doc2 sequences. Amino acid position is marked every hundred amino acids approximately, at the top of each page of the alignment. Splice variants are included and highlighted with black dots where they differ. Intron position and phase is indicated with a coloured bar between amino acids. Black bars indicate phase 0 introns. Red bars indicate phase +1 introns. Blue bars indicate phase +2 introns. Some intron positions are marked with dotted lines. In these cases, transcript sequence covers a gap in the genomic sequence and the intron presence is assumed. The five conserved acidic amino acids in each C2 domain are indicated by black arrows at the top of the alignment. X residues indicate where a portion of sequence is missing.

Format: PDF Size: 215KB Download file

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Open Data