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Summary table

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    FGENESH Genemark Genscan Gene predicted Comments Alignment tblastn
    # begin                        exons # begin end exons # begin end exons
    1 280 669 1 - 1 200 592 1 + 1 280 669 1 - XM_001774108 Physcomitrella patens subsp. patens early light-induced protein 9 (ELIP9) mRNA, complete cds Both pregrams predicted the same gene, but FGENESH predicted minus strand. While, genemark predicted the shorter plus strand. Gene1 Alignment Gene1 BLASTp
                                                                                                A 1701 3128 4 +                                                                                             The best hit of tblastn: No significant similarity Just genemark predicted this region. However, it hit no match. Therefore, This gene might be pseudogene. Alignment tblastn
    2 3948 4690 2 - 2 3948 4690 2 - 2 3948 4690 2 - XM_001774108 Physcomitrella patens subsp. patens early light-induced protein 9 (ELIP9) mRNA, complete cds Interproscan predicted early light-induced protein domain and chlorophyll a,b binding domain Gene2 Alignment Gene2 BLASTp
    3 5869 6603 2 - 3 5014 6603 3 - 3 5869 6603 2 - XM_001774108 Physcomitrella patens subsp. patens early light-induced protein 9(ELIP9) mRNA, complete cds The same domain prediction as in gene 2 Gene3 Alignment Gene3 BLASTp
    4 7818 8569 2 - 4 7506 8569 3 - 4 7381 8569 3 - XM_001774108 Physcomitrella patens subsp. patens early light-induced protein 9(ELIP9) mRNA, complete cds

    The same domain prediction as in gene 2 (Gene 1-4 are the repeat regions shown in dot plot.)

    Gene4 Alignment Gene4 BLASTp
    5 9337 14094 5 + 5.1 9409 11579 4 + 5 9409 15362 5 + Transducin family protein Interproscan predicted WD 40 repeat domain Gene5 Alignment Gene5 BLASTp
                                                                                                5.2 12476 14094 2 +                                                                                             XM_001756373 Physcomitrella patens subsp. patens predicted protein (PHYPADRAFT_24385) mRNA, partial cds FGENESH prediction of the 5th gene covered two genes prediction by genemark (gene 5.1,5.2) Alignment tblastn
    6 14409 16995 5 - 6 14409 16995 6 - 6 15967 16995 4 - 3-hydroxyacyl-CoA dehydrogenase Both programs predicted the same gene with the same length, but different exons. Genemark predicted more exons than FGENESH. Gene6 Alignment Gene6 BLASTp
    7 17202 18382 5 + 7 17202 18382 5 + 7 17202 18293 4 + TatC-like protein sec-independent periplasmic protein translocase TatC domain Gene7 Alignment Gene7 BLASTp
                                                                                                8.1 19414 21489 2 -                                                                                             AC158184 Selaginella moellendorffii clone JGIASXY-5E21, complete sequence Just genemark predicted this gene which is the same as the next predicted gene (8.2). Alignment tblastn
    8 22143 22436 1 - 8.2 21592 22436 3 - 8 21788 22436 2 - AC158184 Selaginella moellendorffii clone JGIASXY-5E21, complete sequence For BLASTp, not match any genes. It might be pseudogene Gene8 Alignment Gene8 BLASTp
                                                                                                B 23480 27219 3 +                                                                                             The best hit of tblastn: no significant similarity found Just genemark predicted this gene which hit no match in NCBI database. Therefore, this might be the psuedogene. Alignment tblastn
                                                                                                                                                                                            9.1 28075 31191 4 -                                              Alignment tblastn
    9 27984 32821 16 - 9 27260 32821 19 - 9.2 31784 32828 2 - ATP-dependent metalloprotease AAA ATPase domain

    Gene9 Alignment  

    Gene9 BLASTp
    10 33215 35059 2 + 10 33140 35059 2 + 10 33140 35059 2 - Glycoside hydrolase family 17 Both programs predicted the same gene with the same two exons and the same stop codon, but different in the start codon.  

    Gene10 Alignment  

    Gene10 BLASTp
    C 35757 37065 6 - c.1 35757 36196 2 - C 35757 37065 3 - AP009673 Lotus japonicus genomic DNA, clone: LjT02J24, TM0401, complete sequence. E-value = 5.1 FGENESH predicted this gene which covered the region of two genes predicted by genemark (C.1, C.2). However, this gene matched the NCBI database with high e-value. Therefore, this gene might be pseudogene. GeneC Alignment GeneC BLASTp
                                                                                                c.2 36525 37001 1 +                                                                                             AP007255 Magnetospirillum magneticum AMB-1 DNA, complete genome E-value = 3.7 The same as comment in C.1 Alignment tblastn
    11 37784 39157 2 + 11 37784 39157 2+ 11 37784 39157 2 + Serine-threonine protein kinase Both programs predicted exactly the same gene.  Gene11 Alignment Gene11 BLASTp
                                                                                                D 39285 39719 1 + D 39282 39705 2 + Ferredoxin Just genemark predicted this gene. It also has low e-value, but it has just one exon. Therefore, it might be pseudogene. GeneD Alignment GeneD BLASTp
    12 39791 43119 8 - 12.1 39791 42449 7 - 12 39791 43119 4 - EU262743 Selaginella moellendorffii putative gibberellin receptor mRNA,complete cds Esterase_lipase superfamily

    Gene12 Alignment  

    Gene12 BLASTp
                                                                                                12.2 42617 43119 3 -                                                                                             EF081679 Picea sitchensis clone WS02813_H13 unknown mRNA The stop codon of FGENESH predicted gene is the same as in gene 12.2 of genemark.   Alignment tblastn
    13 43595 45184 1 - 13 43595 45184 1 - 13 43595 48434 7 - Glyoxal oxidase N-terminal Both programs predicted exactly the same gene.   Gene13 Alignment Gene13 BLASTp
                                                                                                E 45423 45782 2 +                                                                                             AC157217 Pan troglodytes BAC clone CH251-305B5 from chromosome unknown,complete sequence E-value = 6.7 This prediction hit high e-value match. Therefore, this might be pseudogene.   Alignment tblastn
    F 46663 48636 7 - F 46663 48936 7 -                                                                                             Polygalacturonase A Glycohydrolase 28  GeneF Alignment GeneF BLASTp
    14 48850 49940 4 + 14 48850 49940 4 +                                                                                             Bifunctional phosphoribosyl-ATP pyrophosphohydrolase Both programs predicted exactly the same gene.   Gene14 Alignment Gene14 BLASTp
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