XB-IMG-127840
Xenbase Image ID: 127840
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Fig 3. Mis-modeling of genes leads to incorrect sequences in public databases. There are gaps in the Xenopus tropicalis genome assembly in the ifngr2 gene locus, and this has created problems for the gene modeling process. The figure compares alignments for two gene models from different sources and two cDNA based sequences: X. tropicalis gene model A, Ensembl ENSXETT00000000072; gene model B, NCBI XM_002942799.1; EST assembly consensus, Gurdon Xt7.1-TNeu110f24.3; and X. laevis cDNA, NCBI NM_001099874.1. Panel (a) first 400 bp of the assembled EST contig. Visible striations in the EST alignments section indicate the quality of the assembly. The section of the contig sequence missing from the genome sequence is outlined in red. Panel (b) three-way alignment between the 5′-most parts of the EST consensus sequence and the two gene model sequences. Colored boxes and dashed lines link sections of sequence to their positions in the detailed view from the UCSC genome browser page. The red arrow indicates the most likely assembly gap to contain the ‘missing’ sequence. Panel (c) UCSC genome browser view for the whole ifngr2 locus on scaffold_1108, Xt-v4.1, showing BLAT alignments for the EST consensus and gene model sequences. Public EST alignments mapped by UCSC are also shown. Panel (d) a multiple sequence alignment of the resulting translated protein sequences (first ∼70 residues), including a full-length cDNA sequence from Xenopus laevis, showing where the gene model derived protein sequences diverge from the cDNA based sequences. Image published in: Gilchrist MJ (2012) Copyright © 2012 Wiley Periodicals, Inc. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View |