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Daphnia magna DSCAM gene assembly with EvidentialGene

This gene is DSCAM for "Down syndrome cell adhesion molecule", see Human UniProt:O60469 NCBI GeneID:1826, or FruitFly UniProt:Q0E9K4 NCBI GeneID:35652,

These are reference-free, de-novo gene assemblies, made without any other DSCAM gene information, genome-alignment, etc. They appeared in EvidentialGene outputs of the overassembly of Daph. magna mRNA-seq. This is one of the example complex gene loci that is rather difficult to model on genomes accurately. Genome modelling often makes partial models, and models containing *all* exons, not the multiplexed stepwise alternate exons in 3 boxes. See below maps of D. magna genes 2011m and D. pulex genes 2010, with gene-models showing these mistakes.

Approx. 125 valid alternate transcripts were classified by EvidentialGene, from an overassembly of 1072 transcripts of this locus, from one clonal mRNA set. Transcripts have 39 to 20 exons, with proteins of 2006 to 1138 aa. Of these, 58 are Velvet/Oases assembly, 42 from SOAP-denovo assembly, but none from Trinity (which produced partial transcripts of this gene). Longest protein transcripts were assembled from both digital-normalized data and non-normalized, with kmer size in the 57 to 35 range (100bp paired-end Illumina reads). This contrasts with trol gene, where higher kmer ~90 and unnormalized reads with Velvet/O assembled the complete gene.


Daphnia magna DSCAM on Dap. magna genome map. note 3 multiplexed intron-exon blocks, conserved
Daph. magna DSCAM is described in 2011 paper of Dieter Ebert lab, doi:10.1371/journal.pone.0027947

dmagevg7-dscami

Daphnia magna DSCAM on Dap. pulex genome map. note Dap. pulex fragment DSCAM genome-gene models

dmagevg7-dscam-dplxm1

Compare to Fruitfly DSCAM gene,
trol_frufly_alts_ncbi


Developed at the Genome Informatics Lab of Indiana University Biology Department