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Smo8 project

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    FgeneSH results

    FGENESH 2.6 Prediction of potential genes in Dicot_arab genomic DNA

    Seq name: Smo8

    Length of sequence: 96116

    Number of predicted genes 36: in +chain 17, in -chain 19.

    Number of predicted exons 153: in +chain 69, in -chain 84.

    Positions of predicted genes and exons: Variant 1 from 1, Score:3032.145117

      http://linux1.softberry.com/cgi-bin/getfile?/home/apache/tmp/I9bkCv.fgenesh.pdf&application/pdf

    GENSCAN Results

    GENSCAN 1.0 Date run: 21-Oct-108 Time: 20:49:08

    Sequence Smo8 : 96116 bp : 47.80% C+G : Isochore 2 (43 - 51 C+G%)

    Parameter matrix: Arabidopsis.smat

    Number of predicted genes: 25

    Number of Predicted exons: ~217 (counted)

    http://genes.mit.edu/GS/Smo8.pdf

    GeneMark.hmm (Eukaryotic)

    A. thaliana

    Eukariotyc GeneMark.hmm version bp 3.8h August 16, 2007
    Sequence name: Smo8
    Sequence length: 96116 bp
    G+C content: 47.80%
    Matrices file: /home/genmark/euk_ghm.matrices/athaliana_hmm3.0mod
    Tue Oct 21 21:06:15 2008

    Number of Predicted genes: 59

    Number of Predicted exons: ~222 (counted)

    A. gambiae

    Eukariotyc GeneMark.hmm version bp 3.8h August 16, 2007
    Sequence name: Smo8
    Sequence length: 96116 bp
    G+C content: 47.80%
    Matrices file: /home/genmark/euk_ghm.matrices/a_gambiae_05.hmm3.mod
    Thu Oct 23 12:38:16 2008

    Number of Predicted genes: 37

    Number of Predicted Exons: ~101 (counted) 

    Good Gene Preditctions 

    1st Gene        * For Genscan results, polyA-tail and promoter regions included. 

     Program

    Strand

    #Exons  begins  ends  Best Blast hit  e-value 
     FgeneSH - 17 17   4458  

    Histone  deacetylase complex subunit Sin3        

     2e-174        
     Genemark - 13 17   2938  GENE ID: 5940122 SNT1504 | histone deacetylase complex, SIN3 component
    [Physcomitrella patens subsp. patens]    
     0.0    
     Genscan  - 33   17   8478    ref|XP_001776865.1| histone deacetylase complex, SIN3 component [Physcomitrella patens subsp. patens]        0.0      
      

    2nd Gene     

               

     Program Strand  #Exons  begins  ends  Best Blast hit   e-value
     FgeneSH 13  6123  8463 

    Full=Dynamin-related protein 1E         

     0.0      
     Genemark 12  5803  8463  emb|CAO63451.1|  unnamed protein product [Vitis vinifera]       0.0    
     Genscan  33  17  8478   ref|XP_001776865.1| histone deacetylase complex, SIN3 component [Physcomitrella patens subsp. patens]       0.0     

    3rd Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH  1 8687

    9613 

    sp|Q940G6.1|GI1L3_ARATH RecName: Full=Probable gibberellin receptor GID1L3        

    6e-45         

    Genemark  8612 9613  gb|ABK25952.1|  unknown [Picea sitchensis]      5e-62     
    Genscan  8528  9693  gb|ABK25952.1|  unknown [Picea sitchensis]       5e-62      

    4th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
     FgeneSH

    1 

    9760 

    10713 

       

    sp|Q940G6.1|GI1L3_ARATH RecName: Full=Probable gibberellin receptor GID1L3

       

    1e-40         

     Genemark  9760  10713  gb|ABX10756.1|  putative gibberellin receptor [Selaginella moellendorffii]      7e-53     
     Genscan  9720  10748  gb|ABX10756.1|  putative gibberellin receptor [Selaginella moellendorffii]       7e-53     

    5th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
     FgeneSH 10777  11751 

    sp|Q6L545.1|GID1_ORYSJ Gene info RecName: Full=Gibberellin receptor GID1[Oryza sativa Japonica Group]

    5e-30          

     Genemark  10777  11751  gb|ABX10757.1|  putative gibberellin receptor [Selaginella moellendorffii]       2e-53    
     Genscan  1 10751  11797 gb|ABX10757.1|  putative gibberellin receptor [Selaginella moellendorffii]        2e-53    

    6th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH  11876  13308 

    sp|Q7Y1X1|EST_HEVBR Esterase precursor (Early nodule-specific protein homolog)

    2e-56          
    Genemark  11876  13767  gb|ABK27056.1|  unknown [Picea sitchensis]      1e-84     
    Genscan  11  11821  16220  gb|ABK27056.1|  unknown [Picea sitchensis]        7e-71     

    7th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH  19080  20066 

    sp|Q6L545.1|GID1_ORYSJ Gene info RecName: Full=Gibberellin receptor GID1[Oryza sativa Japonica Group]

    3e-54          
    Genemark  19080  20066  tpe|CAP64331.1|  TPA: putative GID1-like gibberellin receptor [Aquilegia formosa
    x Aquilegia pubescens]    
     4e-56   
    Genscan  19044  20420  tpe|CAP64331.1|  TPA: putative GID1-like gibberellin receptor [Aquilegia formosa
    x Aquilegia pubescens]
     4e-56

    8th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH  23461  24503 

    sp|Q6L545.1|GID1_ORYSJ Gene info RecName: Full=Gibberellin receptor GID1; AltName

    5e-35          
    Genemark  23461  24138  gb|ABX10762.1|  gibberellin receptor GID1-like protein [Physcomitrella patens]     3e-38    
    Genscan  20518  25333  dbj|BAC19939.1| putative esterase [Oryza sativa Japonica Group]  1e-41

    9th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH  31484  32470 

    sp|Q6L545.1|GID1_ORYSJ Gene info RecName: Full=Gibberellin receptor GID1[Oryza sativa Japonica Group]

    5e-49          
    Genemark  31484  32470  tpe|CAP64331.1|  TPA: putative GID1-like gibberellin receptor [Aquilegia formosa
    x Aquilegia pubescens]    
     9e-56   
    Genscan  31448  32525  tpe|CAP64331.1|  TPA: putative GID1-like gibberellin receptor [Aquilegia formosa
    x Aquilegia pubescens]
     9e-56

    10th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH 35644  40267 

    sp|Q9SY75.1|PPR30_ARATH Putative pentatricopeptide repeat-containing protein At1g10330

    1e-23           
    Genemark  35644  37266  ref|XP_001763161.1| predicted protein [Physcomitrella patens subsp. patens]      2e-87   
    Genscan  35609  37312  ref|XP_001763161.1|  predicted protein [Physcomitrella patens subsp. patens]    3e-77

    11th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH  12  45533 

    48418 

    sp|Q9AT00.1|NAP11_ARATH RecName: Full=Non-intrinsic ABC protein 11, chloroplastic; Flags: Precursor           

    4e-107           
    Genemark  10  45713  47441   gb|AAC27147.1|AAC27147  Contains similarity to ABC transporter gb|1651790 from Synechocystis
    sp. gb|D90900. [Arabidopsis thaliana]   
    1e-114    
    Genscan  18  40623  47536  gb|AAC27147.1|AAC27147  Contains similarity to ABC transporter gb|1651790 from Synechocystis
    sp. gb|D90900. [Arabidopsis thaliana]  
     1e-88

    12th Gene

               

     Program Strand  #Exons  begins  ends  Best Blast hit  e-value 
    FgeneSH 48810 

    52984 

    sp|Q56XI1.2|PPR25_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At1g09410           

    7e-78           

    Genemark

    -

    1

    48810 

    50671

    50603 

    52984

    gb|ABE80149.1|  Tetratricopeptide-like helical [Medicago truncatula]

    ref|NP_192188.2|  GTP-binding family protein [Arabidopsis thaliana]  

      2e-98

      5e-05

    Genscan  47602  53106  gb|ABE80149.1|  Tetratricopeptide-like helical [Medicago truncatula]  2e-89

    Summary:

    -Many of the Blastp hits came back with putative conserved domains.  These superfamilies were Esterase_lipase, Dynamin_M, RRM, P-loop NTPase, and SGNH_hydrolase.

    -A common hit was with the gibberellin like receptor, so that is probably included in the sequence.

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    Files 3

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     dottup.1.png
    our sequence run through dotter At ~8-10kb-32kb is where a hypothetical gibberellin receptor is located according to Blastx vs. swissprot. From a glance it looks like these repeat regions are in between the exon regions of the hypothetical coded protein. Could be repeats or introns?
    17.31 kB09:35, 30 Oct 2008mandreatActions
     FGeneSH- blastx_vs_swissprt.doc
    Top Blast search of FgeneSH results
    146 kB20:14, 10 Dec 2008afaheyActions
     giberellin insensitve receptor.doc
    Giberellin insensitive receptor
    55 kB20:14, 10 Dec 2008afaheyActions
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