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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-U05010-1
Contig ID Contig-U05010-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U05010-1 (Contig-U05010-1Q) /CSM_Contig/Contig-U05010-1Q.Seq.d
ATATTTTTAAAATCTTTGTAATTATATATATATATATATATATAAATATT
TTTACAATATATTCTAAACTGATNTAATATTTAGTTAAATAAAATTAAAA
AAAAAAAAAAAAAAAAAAAAAAAACAACTTCTTTTGTTTTCTTTTTTTTT
AAAATTATTANTNTTCNNATTTTAGTAACTTTGAATCAATTTCCAAAAAA
AAAAATTTTATTTTTTTCATCACTTAATCANTNNTCCCTGATTAAAATAA
ATAAANGTAAATCCATTTTTTATTTGATATAAAATTTTATGTGTGATGAC
AAGGTTGTTATTTATTATATTTTATAAATGACTTTCAAAATAAAAAANTT
TTTAAAAATTTTAAAAAAAAAAAATAAAAATAAAAAAAATAAATAAATTA
TATCTTATTAATTAGCCAATGTTAAAA
Gap no gap
Contig length 427
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 U05010
List of clone(s) 

est1=SSE507E,1,428
Translated Amino Acid sequence 
iflksl*lyiyiyi*iflqyiln*xni*LNKIKKKKKKKKKTTSFVFFFFKIIXXXILVT
LNQFPKKKILFFSSLNXXSLIKINKXKSIFYLI*nfmcddkvviyyil*mtfkikxflki
lkkknknkknk*iisy*lanvk
Translated Amino Acid sequence (All Frames) 
Frame A:
iflksl*lyiyiyi*iflqyiln*xni*LNKIKKKKKKKKKTTSFVFFFFKIIXXXILVT
LNQFPKKKILFFSSLNXXSLIKINKXKSIFYLI*nfmcddkvviyyil*mtfkikxflki
lkkknknkknk*iisy*lanvk


Frame B:
yf*nlcnyiyiyiykyfynif*tdxifs*iklkkkkkkkkkqlllfsfflkllxfxf**l
*infqkkkfyffhhlixxp*lk*ixvnpffi*ykilcvmtrllfiifyk*lsk*kxf*kf
*kkkikikkinklylin*pmlk


Frame C:
ifkifviiyiyiyiniftiysklx*ylvk*n*kkkkkkkknnffcflff*nyxxsxfsnf
esiskkknfiffit*sxxpd*nk*x*ihflfdikfyv**qgcyllyfindfqnkkxfknf
kkkk*k*kk*inyillisqc*
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05010-1 (Contig-U05010-1Q)
/CSM_Contig/Contig-U05010-1Q.Seq.d
         (427 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05010-1 (Contig-U05010-1Q) /CSM_Contig/Conti...   212  2e-55
Contig-U06398-1 (Contig-U06398-1Q) /CSM_Contig/Conti...    42  5e-04
Contig-U12263-1 (Contig-U12263-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U12505-1 (Contig-U12505-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U12444-1 (Contig-U12444-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U12070-1 (Contig-U12070-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U11964-1 (Contig-U11964-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U11846-1 (Contig-U11846-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U11694-1 (Contig-U11694-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U07022-1 (Contig-U07022-1Q) /CSM_Contig/Conti...    34  0.12

>Contig-U05010-1 (Contig-U05010-1Q) /CSM_Contig/Contig-U05010-1Q.Seq.d
          Length = 427

 Score =  212 bits (107), Expect = 2e-55
 Identities = 119/119 (100%)
 Strand = Plus / Plus

                                                                       
Query: 218 catcacttaatcantnntccctgattaaaataaataaangtaaatccattttttatttga 277
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 218 catcacttaatcantnntccctgattaaaataaataaangtaaatccattttttatttga 277

                                                                      
Query: 278 tataaaattttatgtgtgatgacaaggttgttatttattatattttataaatgactttc 336
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 278 tataaaattttatgtgtgatgacaaggttgttatttattatattttataaatgactttc 336


 Score = 97.6 bits (49), Expect = 9e-21
 Identities = 52/52 (100%)
 Strand = Plus / Plus

                                                              
Query: 45 aatatttttacaatatattctaaactgatntaatatttagttaaataaaatt 96
          ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45 aatatttttacaatatattctaaactgatntaatatttagttaaataaaatt 96


 Score = 63.9 bits (32), Expect = 1e-10
 Identities = 44/44 (100%)
 Strand = Plus / Plus

                                                       
Query: 151 aaaattattantnttcnnattttagtaactttgaatcaatttcc 194
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 151 aaaattattantnttcnnattttagtaactttgaatcaatttcc 194


 Score = 60.0 bits (30), Expect = 2e-09
 Identities = 30/30 (100%)
 Strand = Plus / Plus

                                         
Query: 398 ttatatcttattaattagccaatgttaaaa 427
           ||||||||||||||||||||||||||||||
Sbjct: 398 ttatatcttattaattagccaatgttaaaa 427


 Score = 44.1 bits (22), Expect = 1e-04
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                
Query: 1  atatttttaaaatctttgtaat 22
          ||||||||||||||||||||||
Sbjct: 1  atatttttaaaatctttgtaat 22


>Contig-U06398-1 (Contig-U06398-1Q) /CSM_Contig/Contig-U06398-1Q.Seq.d
          Length = 187

 Score = 42.1 bits (21), Expect = 5e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                
Query: 308 ttatttattatattttataaa 328
           |||||||||||||||||||||
Sbjct: 67  ttatttattatattttataaa 47


>Contig-U12263-1 (Contig-U12263-1Q) /CSM_Contig/Contig-U12263-1Q.Seq.d
          Length = 1743

 Score = 36.2 bits (18), Expect = 0.029
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 45  aatatttttacaatatat 62
           ||||||||||||||||||
Sbjct: 301 aatatttttacaatatat 284


 Score = 28.2 bits (14), Expect = 7.2
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 45  aatatttttacaat 58
           ||||||||||||||
Sbjct: 412 aatatttttacaat 399


 Score = 28.2 bits (14), Expect = 7.2
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                          
Query: 242  ttaaaataaataaa 255
            ||||||||||||||
Sbjct: 1634 ttaaaataaataaa 1647


  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: 10,903
Number of Sequences: 6905
Number of extensions: 10903
Number of successful extensions: 1023
Number of sequences better than 10.0: 320
length of query: 427
length of database: 5,674,871
effective HSP length: 16
effective length of query: 411
effective length of database: 5,564,391
effective search space: 2286964701
effective search space used: 2286964701
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. 7. 7
Homology vs DNA 
Query= Contig-U05010-1 (Contig-U05010-1Q) /CSM_Contig/Contig-U05010-1Q.Seq.d
         (427 letters)

Database: ddbj_B
           105,743,758 sequences; 104,622,809,269 total letters

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

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

(C92514) Dictyostelium discoideum slug cDNA, clone SSE507.         70   3e-48  5
(AU072434) Dictyostelium discoideum slug cDNA, clone SSE507.       62   1e-29  5
(EJ629248) 1092963291969 Global-Ocean-Sampling_GS-29-01-01-1...    34   0.30   3
(EJ640259) 1093011475620 Global-Ocean-Sampling_GS-29-01-01-1...    34   0.38   3
(AM464655) Vitis vinifera contig VV78X130143.3, whole genome...    36   2.9    2
(AC189513) Brassica rapa subsp. pekinensis clone KBrB089L03,...    38   3.5    4
(AC218820) Bos taurus clone CH240-292H10, WORKING DRAFT SEQU...    44   4.4    1
(AC172468) Bos taurus clone CH240-303N23, WORKING DRAFT SEQU...    44   4.4    1
(FI793814) SIR-16C11TF Sisymbrium irio BAC library SIR Sisym...    36   6.6    2

>(C92514) Dictyostelium discoideum slug cDNA, clone SSE507.
          Length = 374

 Score = 69.9 bits (35), Expect(5) = 3e-48
 Identities = 43/47 (91%)
 Strand = Plus / Plus


Query: 218 catcacttaatcantnntccctgattaaaataaataaangtaaatcc 264
           ||||||||||||| |  ||||||||||||||||||||| ||||||||
Sbjct: 164 catcacttaatcaataatccctgattaaaataaataaaagtaaatcc 210

 Score = 63.9 bits (32), Expect(5) = 3e-48
 Identities = 40/44 (90%)
 Strand = Plus / Plus


Query: 151 aaaattattantnttcnnattttagtaactttgaatcaatttcc 194
           |||||||||| | |||  ||||||||||||||||||||||||||
Sbjct: 97  aaaattattactattcctattttagtaactttgaatcaatttcc 140

 Score = 61.9 bits (31), Expect(5) = 3e-48
 Identities = 33/34 (97%)
 Strand = Plus / Plus


Query: 63 tctaaactgatntaatatttagttaaataaaatt 96
          ||||||||||| ||||||||||||||||||||||
Sbjct: 9  tctaaactgatgtaatatttagttaaataaaatt 42

 Score = 58.0 bits (29), Expect(5) = 3e-48
 Identities = 29/29 (100%)
 Strand = Plus / Plus


Query: 399 tatatcttattaattagccaatgttaaaa 427
           |||||||||||||||||||||||||||||
Sbjct: 345 tatatcttattaattagccaatgttaaaa 373

 Score = 34.2 bits (17), Expect(5) = 3e-48
 Identities = 17/17 (100%)
 Strand = Plus / Plus


Query: 125 caacttcttttgttttc 141
           |||||||||||||||||
Sbjct: 71  caacttcttttgttttc 87

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 266,613,632
Number of extensions: 23282555
Number of successful extensions: 1515719
Number of sequences better than 10.0: 9
Length of query: 427
Length of database: 104,622,809,269
Length adjustment: 23
Effective length of query: 404
Effective length of database: 102,190,702,835
Effective search space: 41285043945340
Effective search space used: 41285043945340
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.31
Homology vs Protein 
Query= Contig-U05010-1 (Contig-U05010-1Q) /CSM_Contig/Contig-U05010-1Q.Seq.d
         (427 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 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: 3268448
Number of Hits to DB: 252,291,646
Number of extensions: 2544102
Number of successful extensions: 1506
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1506
Number of HSP's successfully gapped: 0
Length of query: 142
Length of database: 1,061,185,681
Length adjustment: 105
Effective length of query: 37
Effective length of database: 717,998,641
Effective search space: 26565949717
Effective search space used: 26565949717
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: 29 (15.8 bits)
PSORT 

 psg: 0.71  gvh: 0.44  alm: 0.26  top: 0.33  tms: 0.07  mit: 0.49  mip: 0.00
 nuc: 0.45  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  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 : 1.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 24.0 %: mitochondrial
	 24.0 %: nuclear
	 20.0 %: endoplasmic reticulum
	 16.0 %: cytoplasmic
	  8.0 %: Golgi
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U05010-1 is mit
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