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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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Contig-U02687-1
Contig ID Contig-U02687-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U02687-1 (Contig-U02687-1Q) /CSM_Contig/Contig-U02687-1Q.Seq.d
CCCCCCCCCCCCCCCCGGNCCCCTTGGGNAAAAAAAANNAAAAAAAAAAA
AGGAAAAAAAAAGAGAAAAAAAAAAGAAAAAAAAAGAAAAATAAAAAAAT
AAAAGTCTTA
Gap no gap
Contig length 110
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 2
Number of EST 2
Link to clone list U02687
List of clone(s) 

est1=AFJ608Z,-1,107
est2=AFG758Z,1,111
Translated Amino Acid sequence 
PPPPPXPLGKKXXKKKRKKKEKKKRKKKKNKKIKVL
Translated Amino Acid sequence (All Frames) 
Frame A:
ppppprxpwxkkxkkkkgkkkrkkkekkrkikk*ks


Frame B:
pppppgplgxkkxkkkkekkrekkkkkkek*knksl


Frame C:
PPPPPXPLGKKXXKKKRKKKEKKKRKKKKNKKIKVL
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U02687-1 (Contig-U02687-1Q)
/CSM_Contig/Contig-U02687-1Q.Seq.d
         (110 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U02687-1 (Contig-U02687-1Q) /CSM_Contig/Conti...    50  5e-07
Contig-U02879-1 (Contig-U02879-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U14594-1 (Contig-U14594-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U14590-1 (Contig-U14590-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U14556-1 (Contig-U14556-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U14405-1 (Contig-U14405-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U14291-1 (Contig-U14291-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U14289-1 (Contig-U14289-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U12104-1 (Contig-U12104-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U02886-1 (Contig-U02886-1Q) /CSM_Contig/Conti...    32  0.11

>Contig-U02687-1 (Contig-U02687-1Q) /CSM_Contig/Contig-U02687-1Q.Seq.d
          Length = 110

 Score = 50.1 bits (25), Expect = 5e-07
 Identities = 28/28 (100%)
 Strand = Plus / Plus

                                      
Query: 1  ccccccccccccccccggnccccttggg 28
          ||||||||||||||||||||||||||||
Sbjct: 1  ccccccccccccccccggnccccttggg 28


>Contig-U02879-1 (Contig-U02879-1Q) /CSM_Contig/Contig-U02879-1Q.Seq.d
          Length = 192

 Score = 36.2 bits (18), Expect = 0.007
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                            
Query: 1  ccccccccccccccccgg 18
          ||||||||||||||||||
Sbjct: 76 ccccccccccccccccgg 93


 Score = 34.2 bits (17), Expect = 0.027
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                           
Query: 1  ccccccccccccccccg 17
          |||||||||||||||||
Sbjct: 27 ccccccccccccccccg 43


 Score = 32.2 bits (16), Expect = 0.11
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 1   cccccccccccccccc 16
           ||||||||||||||||
Sbjct: 104 cccccccccccccccc 119


 Score = 32.2 bits (16), Expect = 0.11
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 1   cccccccccccccccc 16
           ||||||||||||||||
Sbjct: 103 cccccccccccccccc 118


 Score = 30.2 bits (15), Expect = 0.43
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                         
Query: 2  ccccccccccccccc 16
          |||||||||||||||
Sbjct: 59 ccccccccccccccc 45


 Score = 30.2 bits (15), Expect = 0.43
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                         
Query: 1  ccccccccccccccc 15
          |||||||||||||||
Sbjct: 59 ccccccccccccccc 45


 Score = 26.3 bits (13), Expect = 6.6
 Identities = 13/13 (100%)
 Strand = Plus / Minus

                        
Query: 6   cccccccccccgg 18
           |||||||||||||
Sbjct: 173 cccccccccccgg 161


>Contig-U14594-1 (Contig-U14594-1Q) /CSM_Contig/Contig-U14594-1Q.Seq.d
          Length = 237

 Score = 32.2 bits (16), Expect = 0.11
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 1   cccccccccccccccc 16
           ||||||||||||||||
Sbjct: 197 cccccccccccccccc 212


 Score = 32.2 bits (16), Expect = 0.11
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 1   cccccccccccccccc 16
           ||||||||||||||||
Sbjct: 196 cccccccccccccccc 211


 Score = 32.2 bits (16), Expect = 0.11
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 1   cccccccccccccccc 16
           ||||||||||||||||
Sbjct: 198 cccccccccccccccc 213


 Score = 28.2 bits (14), Expect = 1.7
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 2   cccccccccccccc 15
           ||||||||||||||
Sbjct: 171 cccccccccccccc 158


 Score = 28.2 bits (14), Expect = 1.7
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 3   cccccccccccccc 16
           ||||||||||||||
Sbjct: 171 cccccccccccccc 158


  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: 703
Number of Sequences: 6905
Number of extensions: 703
Number of successful extensions: 472
Number of sequences better than 10.0: 36
length of query: 110
length of database: 5,674,871
effective HSP length: 14
effective length of query: 96
effective length of database: 5,578,201
effective search space: 535507296
effective search space used: 535507296
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2009. 5.20
Homology vs DNA 
Query= Contig-U02687-1 (Contig-U02687-1Q) /CSM_Contig/Contig-U02687-1Q.Seq.d
         (110 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: 1,734,069
Number of extensions: 109587
Number of sequences better than 10.0: 0
Length of query: 110
Length of database: 101,790,757,118
Length adjustment: 22
Effective length of query: 88
Effective length of database: 99,544,435,898
Effective search space: 8759910359024
Effective search space used: 8759910359024
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7.19
Homology vs Protein 
Query= Contig-U02687-1 (Contig-U02687-1Q) /CSM_Contig/Contig-U02687-1Q.Seq.d
         (110 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

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

Lambda     K      H
   0.316    0.124    0.745

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: 67,181,397
Number of extensions: 569629
Number of successful extensions: 3654
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3654
Number of HSP's successfully gapped: 0
Length of query: 36
Length of database: 1,051,180,864
Length adjustment: 10
Effective length of query: 26
Effective length of database: 1,018,815,274
Effective search space: 26489197124
Effective search space used: 26489197124
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: 0.17  gvh: -0.10  alm: 0.89  top: 0.53  tms: 0.00  mit: 0.25  mip: 0.00
 nuc: 1.40  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 

	 72.0 %: nuclear
	 16.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: cytoskeletal

>> prediction for Contig-U02687-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 2
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