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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U06679-1
Contig ID Contig-U06679-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06679-1 (Contig-U06679-1Q) /CSM_Contig/Contig-U06679-1Q.Seq.d
CGCGTCCGAACTTTTTTTATTATTTTTTATATTTTTATATTAATTAATCA
TATTATTTTTTATTATTATTAATATTAATATTAATATAATTTTTATTTAT
ATGCTATAAAATAAATTAAAATTATAATAATTTAAAAAAATACAAAAAAA
AAAAAACCACCCCAAAAAAGGCAATTTTTTTTTTTTTTNCCTTTTTTTTA
AATNAAATTAAATTAAATNCCAATTTNNTTTTNAAATTTAANNTTNANTT
TTTTTTTTTTTTNNGGGGTCCCNAAAAAAAAAAAAAAAAAAGGGGGGGGN
TTTTTAAAAAANNNANTTTTTAAAAANNNNTTTTTTAAAAAAAAA
Gap no gap
Contig length 345
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U06679
List of clone(s) 

est1=VSF123F,1,346
Translated Amino Acid sequence 
rpnffyyflyfyin*syyfllllilili*flficykin*NYNNLKKYKKKKTTPKKAIFF
FFXFFLNXIKLNXNXXXKFXXXFFFFXXGPXKKKKKRGGXFKKXXF*kxxf*kk
Translated Amino Acid sequence (All Frames) 
Frame A:
rvrtffiifyifilinhiifyyy*y*y*ynfylyaik*ikiiii*kntkkkkppqkrqff
ffxpff*xkln*xpixfxnlxxxffffxgvpkkkkkkgggflkxxxfkxxffkkk


Frame B:
aselfllffifly*liilffiiinininiifiyml*nklkl**fkkiqkkknhpkkgnff
ffxlffkxn*ikxqfxfxi*xxxffffxgsxkkkkkkggxf*kxxflkxxflkk


Frame C:
rpnffyyflyfyin*syyfllllilili*flficykin*NYNNLKKYKKKKTTPKKAIFF
FFXFFLNXIKLNXNXXXKFXXXFFFFXXGPXKKKKKRGGXFKKXXF*kxxf*kk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06679-1 (Contig-U06679-1Q)
/CSM_Contig/Contig-U06679-1Q.Seq.d
         (345 letters)

Database: CSM
           6905 sequences; 5,674,871 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06679-1 (Contig-U06679-1Q) /CSM_Contig/Conti...    54  1e-07
Contig-U14738-1 (Contig-U14738-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U13315-1 (Contig-U13315-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U12088-1 (Contig-U12088-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U11245-1 (Contig-U11245-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U11158-1 (Contig-U11158-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U11133-1 (Contig-U11133-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U06929-1 (Contig-U06929-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U06711-1 (Contig-U06711-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U06615-1 (Contig-U06615-1Q) /CSM_Contig/Conti...    32  0.37

>Contig-U06679-1 (Contig-U06679-1Q) /CSM_Contig/Contig-U06679-1Q.Seq.d
          Length = 345

 Score = 54.0 bits (27), Expect = 1e-07
 Identities = 42/42 (100%)
 Strand = Plus / Plus

                                                     
Query: 200 aaatnaaattaaattaaatnccaatttnnttttnaaatttaa 241
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 200 aaatnaaattaaattaaatnccaatttnnttttnaaatttaa 241


 Score = 36.2 bits (18), Expect = 0.024
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 157 ccaccccaaaaaaggcaa 174
           ||||||||||||||||||
Sbjct: 157 ccaccccaaaaaaggcaa 174


>Contig-U14738-1 (Contig-U14738-1Q) /CSM_Contig/Contig-U14738-1Q.Seq.d
          Length = 618

 Score = 32.2 bits (16), Expect = 0.37
 Identities = 18/19 (94%)
 Strand = Plus / Plus

                              
Query: 200 aaatnaaattaaattaaat 218
           |||| ||||||||||||||
Sbjct: 402 aaattaaattaaattaaat 420


 Score = 28.2 bits (14), Expect = 5.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 205 aaattaaattaaat 218
           ||||||||||||||
Sbjct: 421 aaattaaattaaat 434


>Contig-U13315-1 (Contig-U13315-1Q) /CSM_Contig/Contig-U13315-1Q.Seq.d
          Length = 208

 Score = 32.2 bits (16), Expect = 0.37
 Identities = 18/19 (94%)
 Strand = Plus / Minus

                              
Query: 200 aaatnaaattaaattaaat 218
           |||| ||||||||||||||
Sbjct: 49  aaattaaattaaattaaat 31


 Score = 32.2 bits (16), Expect = 0.37
 Identities = 18/19 (94%)
 Strand = Plus / Minus

                              
Query: 200 aaatnaaattaaattaaat 218
           |||| ||||||||||||||
Sbjct: 39  aaattaaattaaattaaat 21


 Score = 32.2 bits (16), Expect = 0.37
 Identities = 18/19 (94%)
 Strand = Plus / Minus

                              
Query: 200 aaatnaaattaaattaaat 218
           |||| ||||||||||||||
Sbjct: 54  aaattaaattaaattaaat 36


 Score = 32.2 bits (16), Expect = 0.37
 Identities = 18/19 (94%)
 Strand = Plus / Minus

                              
Query: 200 aaatnaaattaaattaaat 218
           |||| ||||||||||||||
Sbjct: 44  aaattaaattaaattaaat 26


 Score = 30.2 bits (15), Expect = 1.5
 Identities = 17/18 (94%)
 Strand = Plus / Minus

                             
Query: 200 aaatnaaattaaattaaa 217
           |||| |||||||||||||
Sbjct: 34  aaattaaattaaattaaa 17


  Database: CSM
    Posted date:  Jun 9, 2004  7:35 PM
  Number of letters in database: 5,674,871
  Number of sequences in database:  6905
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 770
Number of Sequences: 6905
Number of extensions: 770
Number of successful extensions: 188
Number of sequences better than 10.0: 61
length of query: 345
length of database: 5,674,871
effective HSP length: 15
effective length of query: 330
effective length of database: 5,571,296
effective search space: 1838527680
effective search space used: 1838527680
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
dna update 2008.11. 9
Homology vs DNA 
Query= Contig-U06679-1 (Contig-U06679-1Q) /CSM_Contig/Contig-U06679-1Q.Seq.d
         (345 letters)

Database: ddbj_A
           92,845,959 sequences; 95,242,211,685 total letters

Searching..................................................done

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(AU264743) Dictyostelium discoideum vegetative cDNA clone:VS...    54   2e-08  2

>(AU264743) Dictyostelium discoideum vegetative cDNA clone:VSF123,
           5' end single read.
          Length = 346

 Score = 54.0 bits (27), Expect(2) = 2e-08
 Identities = 42/42 (100%)
 Strand = Plus / Plus


Query: 200 aaatnaaattaaattaaatnccaatttnnttttnaaatttaa 241
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 200 aaatnaaattaaattaaatnccaatttnnttttnaaatttaa 241

 Score = 36.2 bits (18), Expect(2) = 2e-08
 Identities = 18/18 (100%)
 Strand = Plus / Plus


Query: 157 ccaccccaaaaaaggcaa 174
           ||||||||||||||||||
Sbjct: 157 ccaccccaaaaaaggcaa 174

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 49,562,208
Number of extensions: 3567958
Number of successful extensions: 342888
Number of sequences better than 10.0: 1
Length of query: 345
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 322
Effective length of database: 93,106,754,628
Effective search space: 29980374990216
Effective search space used: 29980374990216
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06679-1 (Contig-U06679-1Q) /CSM_Contig/Contig-U06679-1Q.Seq.d
         (345 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

Searching..................................................done

 ***** No hits found ******

Lambda     K      H
   0.318    0.134    0.401

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3204285
Number of Hits to DB: 64,475,089
Number of extensions: 1181627
Number of successful extensions: 28
Number of sequences better than 10.0: 0
Number of HSP's gapped: 28
Number of HSP's successfully gapped: 0
Length of query: 115
Length of database: 1,040,966,779
Length adjustment: 82
Effective length of query: 33
Effective length of database: 778,215,409
Effective search space: 25681108497
Effective search space used: 25681108497
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 28 (15.4 bits)
PSORT 

 psg: 0.55  gvh: 0.45  alm: 0.39  top: 0.53  tms: 0.00  mit: 0.38  mip: 0.00
 nuc: 0.34  erl: 0.00  erm: 0.40  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 64.0 %: nuclear
	 28.0 %: cytoplasmic
	  8.0 %: mitochondrial

>> prediction for Contig-U06679-1 is nuc
VS (DIR, S) 1
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0