Phosphatase GeneID MbreP095
MbreP095 and part of Mbre096 are identical in protein sequence. To find out whether they are encoded by two genes,
1. Obtain the genomic sequence. MbreP095 and Mbre096 are from 16302 and 35258 in JGI monosiga. You can find them by BLASTing the two sequences via JGI server. Then, go to the gene page and click "To Genome Browser". On the genome browser page, zoom in and zoom out to select the regions to compare, then click "DNA" to get the sequences.
2. Compare the genomic sequences with BL2SEQ via NCBI BLAST server. The alignment is 537 bp and identity is 100%. But, the downstream region of MbreP095 does not align with the genomic sequence of MbreP096; the upstream region has a 50 bp gap.
The next question is whether MbreP095 is a real protein-coding gene.
As shown in the genome browser, MbreP095 is not supported by EST data. The JGI monosiga genome project has predicted two ab initio gene models. The first one overlaps with and is longer than MbreP095; the second one does not overlap with MbreP095 but is supported by EST data. The protein sequences are shown below. I BLASTed the two sequences against NR database via NCBI BLAST server. The best hits of the first one is only 7% coverage at the phosphatase domain and identity is around 85%. The second one has few hits. The best hit from S. Rosetta, whose E-value is just below e-5.
>jgi|Monbr1|24699|fgenesh2_pg.scaffold_7000247 desc="ab initio monosiga parameters" MFQSLRMMGKSLSSAAEAGDVDAVQSLLSSSFKGPGKRAQSINDKVSTCSSLKGSPLCIVPDEDGCTPLH KAALNSHFLQGHLAVVELLLTANADVNATDKNGMTPLHMAAFNNQHDVARLLLDGGADVSVTSTRAGETP LHISANVGHVEVMQTLINYGADPLEETKDGTSPLELAAGAGHLDMTRFLLSLRDLGYEILPPPSRKSHKK GLICTRFSLMLRVIAGFDIDYPSGSGTALSVAAMKRKMDCVKALLLRGADTNLPEGSAQHERLVELLEDL DNASSLELCNLLDTDRRPSELGAIIHMAAGLSGSLDGGNADAIASDGQAAPRMSSLRALRNKIGMRSARS NSDTDAASTESNPVVEAEAPPIPSPYQPEPNEEPKPADPELEDPEAKPEAETIEPETIKSEPEAIELETV NREASKAEAGGDLEAAGEPSTSSTTARVETSDDTSIEDTSPDTAASAKEATDAKASAAMTAQPDDESPPP VRASISIPPPPPSTAPAADAEQSERADDAETSSEGSGTAGTPLAEDTRHADVSILRDAEPQAGASSASRM RLFSRGASAPAPAVPRPVTHKDLLKEGPLWKKPQIRTGKINVNNKARLRWFVLQETTLSYYDYSPESTKK RIGKIKGCIPLNTVLQVQASHGEGDEATRCFEVIQEDAALFCVAGNMAERDAWVTAICRAWAAAETLIKP QNRLPMPESTEGEAQPPPLPVPYADQATENQATRERGFTASVKNRASLKASASQLARQQELEREELGMVD MSIDLTEAEIRGLCVKSREIFLNQPILLELEAPLRICGDTHGQYYDLLRMFEYGGFPPESNYLFLGDYVD RGKQICKSKTEQELCRLQKKKHSRRPITAAKPTYPLKKKAASIRVSRQPAKPTAKPTGKAARPPSSVSLC GSKHEKEQSERKGG*
>jgi|Monbr1|7514|fgenesh1_pg.scaffold_7000246 desc="ab initio human parameters" MVAMPLGWVPMALGVGTVATLAVWRRTLTLDGGLAAFPVGLAVGLAGWRETLMLAAFFLSGSVATKALHK YNRSTNALDTDVKTAVFGVAGSIVDSILGQLLQGPAQMAAQPARWKQLNVLVNLISSLVMAGAAMFSFWH HPPVIVGALVASVAFLFLLYRHE*
