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Supplementary material
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Genet. Mol. Res. (2004) 3(4): 532-544. [pdf]
A bioinformatics analysis of alternative exon usage in human genes
coding for extracellular matrix proteins
| Supplementary
File 1 |
ECM keywords | text file containing the list of keywords related to cell adhesion and extracellular matrix proteins used to separate the ECM set |
| Supplementary
File 2 |
multiple exon event example | UCSC's genome browser output displaying a real example of a long multiple exon event. AU117672 (“Your query sequence from BLAT search”) skipping many internal exons of reference mRNA X14420, gene symbol COL3A1 |
| Supplementary
File 3 |
simulation |
results of the simulation of the effect of random AEU events in protein domains using an artificial sequence. Table SI shows results of a simulation where we varied the density of domains. Results of a simulation of the effect of AEU event length on the frequency of domains affected by AEU are displayed in Table SII. Table SIII brings data on a simulation varying the lengths of events. |
| Supplementary
File 4 |
Supplementary Tables |
Table S1 shows cluster sizes of all
sets, Table S2 distribution of exon-intron structures per cluster,
Table S3 brings the distributions of number of events per exon-intron
structure, Table S4 shows data on CDS/UTR location of AEU events, Table
S5 and Table S6 shows the distribution of number of exons per
event in all sets. |
| Supplementary
File 5 |
list of "long" genes in the
ECM set |
nucleotide GenBank accession numbers
of reference full-insert cDNAs with more than 25 exons |