Missing gene in synteny? (use-case)
MtFTa1 (MtrunA17Chr7_39606925_39618489, position 39606925-39609016) has orthologs in Ps3:
- "Psat3g090720" 186553477 186556218
- "Psat3g090680" 186528296 186540030 We know there is a block spanning these regions (for now called mcscanx_block_1191, with 314 gene pairs.
g.chromosome min(g.start) max(g.stop) s.nb_genes
"Ps3" 110938472 199624819 314
"Mt7" 38006676 46632808 314
Since the orthologous genes are on the same chromosomes and both chromosomes are syntenic, why isn't MtFTa1 included in the syntenic block? Need to observe the region more precisely. Also consider https://github.com/wyp1125/MCScanX/issues/34 if there is no answer.