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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-U13219-1
Contig ID Contig-U13219-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13219-1 (Contig-U13219-1Q) /CSM_Contig/Contig-U13219-1Q.Seq.d
ATAAATAAATAAATAAGNAATTACCACCATAATTTTTAAAATTTTAGATA
ATATTAACATTATAATAAATAAAATAGATAATAAAATAAAATAAAAAAAA
AANNNNNNNNN
Gap no gap
Contig length 111
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 5686662
End point 5686561
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U13219
List of clone(s) 

est1=SHB511F,1,102
Translated Amino Acid sequence 
*ink*XITTIIFKILDNINIIINKIDNKIK*kkxxx
Translated Amino Acid sequence (All Frames) 
Frame A:
ink*ixnyhhnf*nfr*y*hynk*nr**nkikkkxxx


Frame B:
*ink*XITTIIFKILDNINIIINKIDNKIK*kkxxx


Frame C:
k*inkxlpp*flkf*iiltl**ik*iik*nkkkxxx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13219-1 (Contig-U13219-1Q)
/CSM_Contig/Contig-U13219-1Q.Seq.d
         (111 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13219-1 (Contig-U13219-1Q) /CSM_Contig/Conti...    58  2e-09
Contig-U12594-1 (Contig-U12594-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U14682-1 (Contig-U14682-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U11608-1 (Contig-U11608-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U11397-1 (Contig-U11397-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U09714-1 (Contig-U09714-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U05084-1 (Contig-U05084-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U03520-1 (Contig-U03520-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U14607-1 (Contig-U14607-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U14383-1 (Contig-U14383-1Q) /CSM_Contig/Conti...    32  0.11

>Contig-U13219-1 (Contig-U13219-1Q) /CSM_Contig/Contig-U13219-1Q.Seq.d
          Length = 111

 Score = 58.0 bits (29), Expect = 2e-09
 Identities = 32/32 (100%)
 Strand = Plus / Plus

                                          
Query: 1  ataaataaataaataagnaattaccaccataa 32
          ||||||||||||||||||||||||||||||||
Sbjct: 1  ataaataaataaataagnaattaccaccataa 32


>Contig-U12594-1 (Contig-U12594-1Q) /CSM_Contig/Contig-U12594-1Q.Seq.d
          Length = 977

 Score = 36.2 bits (18), Expect = 0.007
 Identities = 20/21 (95%)
 Strand = Plus / Plus

                                
Query: 1   ataaataaataaataagnaat 21
           ||||||||||||||||| |||
Sbjct: 520 ataaataaataaataagtaat 540


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

                           
Query: 1   ataaataaataaataa 16
           ||||||||||||||||
Sbjct: 492 ataaataaataaataa 507


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

                           
Query: 1   ataaataaataaataa 16
           ||||||||||||||||
Sbjct: 428 ataaataaataaataa 443


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

                           
Query: 1   ataaataaataaataa 16
           ||||||||||||||||
Sbjct: 432 ataaataaataaataa 447


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

                          
Query: 1   ataaataaataaata 15
           |||||||||||||||
Sbjct: 436 ataaataaataaata 450


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

                         
Query: 3   aaataaataaataa 16
           ||||||||||||||
Sbjct: 477 aaataaataaataa 490


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

                         
Query: 3   aaataaataaataa 16
           ||||||||||||||
Sbjct: 490 aaataaataaataa 503


 Score = 26.3 bits (13), Expect = 6.7
 Identities = 13/13 (100%)
 Strand = Plus / Plus

                        
Query: 4   aataaataaataa 16
           |||||||||||||
Sbjct: 541 aataaataaataa 553


 Score = 26.3 bits (13), Expect = 6.7
 Identities = 13/13 (100%)
 Strand = Plus / Plus

                        
Query: 1   ataaataaataaa 13
           |||||||||||||
Sbjct: 479 ataaataaataaa 491


 Score = 26.3 bits (13), Expect = 6.7
 Identities = 13/13 (100%)
 Strand = Plus / Plus

                        
Query: 4   aataaataaataa 16
           |||||||||||||
Sbjct: 519 aataaataaataa 531


 Score = 26.3 bits (13), Expect = 6.7
 Identities = 13/13 (100%)
 Strand = Plus / Plus

                        
Query: 1   ataaataaataaa 13
           |||||||||||||
Sbjct: 542 ataaataaataaa 554


>Contig-U14682-1 (Contig-U14682-1Q) /CSM_Contig/Contig-U14682-1Q.Seq.d
          Length = 2904

 Score = 34.2 bits (17), Expect = 0.028
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 1    ataaataaataaataag 17
            |||||||||||||||||
Sbjct: 2456 ataaataaataaataag 2440


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

                            
Query: 1    ataaataaataaataa 16
            ||||||||||||||||
Sbjct: 2460 ataaataaataaataa 2445


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

                           
Query: 2    taaataaataaataa 16
            |||||||||||||||
Sbjct: 2463 taaataaataaataa 2449


 Score = 26.3 bits (13), Expect = 6.7
 Identities = 13/13 (100%)
 Strand = Plus / Minus

                         
Query: 1    ataaataaataaa 13
            |||||||||||||
Sbjct: 2580 ataaataaataaa 2568


 Score = 26.3 bits (13), Expect = 6.7
 Identities = 13/13 (100%)
 Strand = Plus / Minus

                         
Query: 4    aataaataaataa 16
            |||||||||||||
Sbjct: 2581 aataaataaataa 2569


  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: 5077
Number of Sequences: 6905
Number of extensions: 5077
Number of successful extensions: 3428
Number of sequences better than 10.0: 845
length of query: 111
length of database: 5,674,871
effective HSP length: 14
effective length of query: 97
effective length of database: 5,578,201
effective search space: 541085497
effective search space used: 541085497
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 2008.12. 7
Homology vs DNA 
Query= Contig-U13219-1 (Contig-U13219-1Q) /CSM_Contig/Contig-U13219-1Q.Seq.d
         (111 letters)

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

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

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

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 0
Number of sequences better than 10.0: 0
Length of query: 111
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 89
Effective length of database: 93,199,600,587
Effective search space: 8294764452243
Effective search space used: 8294764452243
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13219-1 (Contig-U13219-1Q) /CSM_Contig/Contig-U13219-1Q.Seq.d
         (111 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: 54,742,381
Number of extensions: 904765
Number of successful extensions: 23
Number of sequences better than 10.0: 0
Number of HSP's gapped: 23
Number of HSP's successfully gapped: 0
Length of query: 37
Length of database: 1,051,180,864
Length adjustment: 11
Effective length of query: 26
Effective length of database: 1,015,578,715
Effective search space: 26405046590
Effective search space used: 26405046590
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: 0.64  gvh: 0.12  alm: 0.39  top: 0.53  tms: 0.00  mit: 0.22  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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 

	 40.0 %: cytoplasmic
	 36.0 %: nuclear
	  8.0 %: cytoskeletal
	  4.0 %: extracellular, including cell wall
	  4.0 %: mitochondrial
	  4.0 %: vacuolar
	  4.0 %: plasma membrane

>> prediction for Contig-U13219-1 is cyt
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) 0
SH (FL, L) 1
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0