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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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Contig-U01610-1
Contig ID Contig-U01610-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01610-1 (Contig-U01610-1Q) /CSM_Contig/Contig-U01610-1Q.Seq.d
GTTTTCCATTTATTTAAATTTAAATTTAAATTTTTTTTTTTAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 121
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 U01610
List of clone(s) 

est1=SSC486Z,1,122
Translated Amino Acid sequence 
VFHLFKFKFKFFFLKKKKKKKKKKKKKKKKKKKKKKKKKK
Translated Amino Acid sequence (All Frames) 
Frame A:
VFHLFKFKFKFFFLKKKKKKKKKKKKKKKKKKKKKKKKKK


Frame B:
fsiylnlnlnfff*kkkkkkkkkkkkkkkkkkkkkkkkkk


Frame C:
fpfi*i*i*ifffkkkkkkkkkkkkkkkkkkkkkkkkkk
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01610-1 (Contig-U01610-1Q)
/CSM_Contig/Contig-U01610-1Q.Seq.d
         (121 letters)

Database: CSM
           8361 sequences; 7,895,291 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01610-1 (Contig-U01610-1Q) /CSM_Contig/Conti...    82  2e-16
Contig-U04210-1 (Contig-U04210-1Q) /CSM_Contig/Conti...    50  7e-07
Contig-U10820-1 (Contig-U10820-1Q) /CSM_Contig/Conti...    46  1e-05
Contig-U10805-1 (Contig-U10805-1Q) /CSM_Contig/Conti...    46  1e-05
Contig-U14271-1 (Contig-U14271-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U12192-1 (Contig-U12192-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U11221-1 (Contig-U11221-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U09472-1 (Contig-U09472-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U06368-1 (Contig-U06368-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U05848-1 (Contig-U05848-1Q) /CSM_Contig/Conti...    34  0.042

>Contig-U01610-1 (Contig-U01610-1Q) /CSM_Contig/Contig-U01610-1Q.Seq.d
          Length = 121

 Score = 81.8 bits (41), Expect = 2e-16
 Identities = 41/41 (100%)
 Strand = Plus / Plus

                                                   
Query: 1  gttttccatttatttaaatttaaatttaaattttttttttt 41
          |||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  gttttccatttatttaaatttaaatttaaattttttttttt 41


 Score = 40.1 bits (20), Expect = 7e-04
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                              
Query: 12 atttaaatttaaatttaaat 31
          ||||||||||||||||||||
Sbjct: 31 atttaaatttaaatttaaat 12


 Score = 36.2 bits (18), Expect = 0.011
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                            
Query: 16 aaatttaaatttaaattt 33
          ||||||||||||||||||
Sbjct: 33 aaatttaaatttaaattt 16


>Contig-U04210-1 (Contig-U04210-1Q) /CSM_Contig/Contig-U04210-1Q.Seq.d
          Length = 687

 Score = 50.1 bits (25), Expect = 7e-07
 Identities = 31/33 (93%)
 Strand = Plus / Minus

                                            
Query: 9   tttatttaaatttaaatttaaattttttttttt 41
           ||||||||||||||| ||||| |||||||||||
Sbjct: 135 tttatttaaatttaattttaatttttttttttt 103


 Score = 28.2 bits (14), Expect = 2.6
 Identities = 17/18 (94%)
 Strand = Plus / Plus

                             
Query: 14  ttaaatttaaatttaaat 31
           ||||| ||||||||||||
Sbjct: 115 ttaaaattaaatttaaat 132


>Contig-U10820-1 (Contig-U10820-1Q) /CSM_Contig/Contig-U10820-1Q.Seq.d
          Length = 1642

 Score = 46.1 bits (23), Expect = 1e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                   
Query: 12   atttaaatttaaatttaaatttt 34
            |||||||||||||||||||||||
Sbjct: 1547 atttaaatttaaatttaaatttt 1569


 Score = 44.1 bits (22), Expect = 4e-05
 Identities = 22/22 (100%)
 Strand = Plus / Minus

                                  
Query: 12   atttaaatttaaatttaaattt 33
            ||||||||||||||||||||||
Sbjct: 1566 atttaaatttaaatttaaattt 1545


 Score = 44.1 bits (22), Expect = 4e-05
 Identities = 25/26 (96%)
 Strand = Plus / Plus

                                      
Query: 8    atttatttaaatttaaatttaaattt 33
            |||| |||||||||||||||||||||
Sbjct: 1537 atttttttaaatttaaatttaaattt 1562


 Score = 38.2 bits (19), Expect = 0.003
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                               
Query: 12   atttaaatttaaatttaaa 30
            |||||||||||||||||||
Sbjct: 1560 atttaaatttaaatttaaa 1542


 Score = 36.2 bits (18), Expect = 0.011
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                              
Query: 16   aaatttaaatttaaattt 33
            ||||||||||||||||||
Sbjct: 1568 aaatttaaatttaaattt 1551


  Database: CSM
    Posted date:  Jun 7, 2004  8:33 AM
  Number of letters in database: 7,895,291
  Number of sequences in database:  8361
  
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: 91,917
Number of Sequences: 8361
Number of extensions: 91917
Number of successful extensions: 6954
Number of sequences better than 10.0: 907
length of query: 121
length of database: 7,895,291
effective HSP length: 15
effective length of query: 106
effective length of database: 7,769,876
effective search space: 823606856
effective search space used: 823606856
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 2009. 5. 3
Homology vs DNA 
Query= Contig-U01610-1 (Contig-U01610-1Q) /CSM_Contig/Contig-U01610-1Q.Seq.d
         (121 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

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

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 0
Number of sequences better than 10.0: 0
Length of query: 121
Length of database: 101,790,757,118
Length adjustment: 22
Effective length of query: 99
Effective length of database: 99,544,435,898
Effective search space: 9854899153902
Effective search space used: 9854899153902
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01610-1 (Contig-U01610-1Q) /CSM_Contig/Contig-U01610-1Q.Seq.d
         (121 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 14,857,034
Number of extensions: 12091
Number of sequences better than 10.0: 0
Number of HSP's gapped: 0
Number of HSP's successfully gapped: 0
Length of query: 40
Length of database: 1,051,180,864
Length adjustment: 14
Effective length of query: 26
Effective length of database: 1,005,869,038
Effective search space: 26152594988
Effective search space used: 26152594988
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: 24 (13.9 bits)
PSORT 

 psg: 0.53  gvh: 0.04  alm: 0.56  top: 0.53  tms: 0.00  mit: 0.33  mip: 0.00
 nuc: 2.71  erl: 0.00  erm: 0.80  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 

	 76.0 %: nuclear
	 12.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: cytoskeletal

>> prediction for Contig-U01610-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 1
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