Mark at 04:42, 30 September 2015

2015-09-30T04:42:49Z

Mark: Created page with "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 f..."

2015-09-30T04:22:38Z

Created page with "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 f..."

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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 [http://genome.jgi.doe.gov/cgi-bin/dispGeneModel?db=Monbr1&id=16302 16302] and [http://genome.jgi.doe.gov/cgi-bin/dispGeneModel?db=Monbr1&id=35258 35258] in JGI monosiga. You can find them by BLASTing the two sequences via [http://genome.jgi.doe.gov/pages/blast-query.jsf?db=Monbr1 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.

As shown in the [http://genome.jgi.doe.gov/cgi-bin/browserLoad/?db=Monbr1&position=scaffold_7:1090554-1093263 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.

>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
MVAMPLGWVPMALGVGTVATLAVWRRTLTLDGGLAAFPVGLAVGLAGWRETLMLAAFFLSGSVATKALHK
YNRSTNALDTDVKTAVFGVAGSIVDSILGQLLQGPAQMAAQPARWKQLNVLVNLISSLVMAGAAMFSFWH
HPPVIVGALVASVAFLFLLYRHE*

@@ Line 5: / Line 5: @@
 . 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.
-As shown in the [http://genome.jgi.doe.gov/cgi-bin/browserLoad/?db=Monbr1&position=scaffold_7:1090554-1093263 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.
+The next question is whether MbreP095 is a real protein-coding gene.
 >jgi|Monbr1|24699|fgenesh2_pg.scaffold_7000247 desc="ab initio monosiga parameters"
@@ Line 23: / Line 25: @@
 GSKHEKEQSERKGG*
->jgi|Monbr1|7514|fgenesh1_pg.scaffold_7000246
+>jgi|Monbr1|7514|fgenesh1_pg.scaffold_7000246 desc="ab initio human parameters"
 MVAMPLGWVPMALGVGTVATLAVWRRTLTLDGGLAAFPVGLAVGLAGWRETLMLAAFFLSGSVATKALHK
 YNRSTNALDTDVKTAVFGVAGSIVDSILGQLLQGPAQMAAQPARWKQLNVLVNLISSLVMAGAAMFSFWH
 HPPVIVGALVASVAFLFLLYRHE*

Phosphatase GeneID MbreP095 - Revision history

Mark at 04:42, 30 September 2015

Mark: Created page with "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 f..."