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Dicty_cDB
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U04544-1
Contig ID Contig-U04544-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U04544-1 (Contig-U04544-1Q) /CSM_Contig/Contig-U04544-1Q.Seq.d
TAATTAATTAATTTAAAAAAAAAAAAAAAAAATTAAAAAAAAATAAAAAA
AATGGAATTTAAAAAAAAAAAAAAAAAAAAACAAAGTTGTAATTTTTCAA
TAAAAGATANCTTAAAAGGGAAAAATTGAGATTGAAGCAAGATTANATAT
ACTGAGACNACAAAAATGATGAAAATCAAAAAAAAAATAAAAATAAAAAA
ATTTAAAATTTAAAATTTA
Gap no gap
Contig length 219
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 U04544
List of clone(s) 

est1=SSB374F,1,220
Translated Amino Acid sequence 
*linlkkkkkn*KKIKKMEFKKKKKKKQSCNFSIKDXLKGKN*d*skixytettkmmkik
kkikikkfki*nl
Translated Amino Acid sequence (All Frames) 
Frame A:
*linlkkkkkn*KKIKKMEFKKKKKKKQSCNFSIKDXLKGKN*d*skixytettkmmkik
kkikikkfki*nl


Frame B:
n*li*kkkkkikkk*kkwnlkkkkkknkvvifq*kix*kgkieiearlxilrxqk**ksk
kk*k*knlkfki


Frame C:
in*fkkkkkklkknkkngi*kkkkkktkl*ffnkrxlkreklrlkqdxiy*dxkndenqk
knknkki*nlkf
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04544-1 (Contig-U04544-1Q)
/CSM_Contig/Contig-U04544-1Q.Seq.d
         (219 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04544-1 (Contig-U04544-1Q) /CSM_Contig/Conti...   141  3e-34
Contig-U14801-1 (Contig-U14801-1Q) /CSM_Contig/Conti...    36  0.015
Contig-U05084-1 (Contig-U05084-1Q) /CSM_Contig/Conti...    36  0.015
Contig-U02000-1 (Contig-U02000-1Q) /CSM_Contig/Conti...    36  0.015
Contig-U10831-1 (Contig-U10831-1Q) /CSM_Contig/Conti...    34  0.058
Contig-U07046-1 (Contig-U07046-1Q) /CSM_Contig/Conti...    34  0.058
Contig-U06984-1 (Contig-U06984-1Q) /CSM_Contig/Conti...    34  0.058
Contig-U14308-1 (Contig-U14308-1Q) /CSM_Contig/Conti...    32  0.23
Contig-U13756-1 (Contig-U13756-1Q) /CSM_Contig/Conti...    32  0.23
Contig-U12801-1 (Contig-U12801-1Q) /CSM_Contig/Conti...    32  0.23

>Contig-U04544-1 (Contig-U04544-1Q) /CSM_Contig/Contig-U04544-1Q.Seq.d
          Length = 219

 Score =  141 bits (71), Expect = 3e-34
 Identities = 77/77 (100%)
 Strand = Plus / Plus

                                                                       
Query: 82  caaagttgtaatttttcaataaaagatancttaaaagggaaaaattgagattgaagcaag 141
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 82  caaagttgtaatttttcaataaaagatancttaaaagggaaaaattgagattgaagcaag 141

                            
Query: 142 attanatatactgagac 158
           |||||||||||||||||
Sbjct: 142 attanatatactgagac 158


 Score = 36.2 bits (18), Expect = 0.015
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 202 tttaaaatttaaaattta 219
           ||||||||||||||||||
Sbjct: 202 tttaaaatttaaaattta 219


 Score = 30.2 bits (15), Expect = 0.90
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 205 aaaatttaaaattta 219
           |||||||||||||||
Sbjct: 198 aaaatttaaaattta 212


 Score = 28.2 bits (14), Expect = 3.6
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                        
Query: 1  taattaattaattt 14
          ||||||||||||||
Sbjct: 1  taattaattaattt 14


>Contig-U14801-1 (Contig-U14801-1Q) /CSM_Contig/Contig-U14801-1Q.Seq.d
          Length = 749

 Score = 36.2 bits (18), Expect = 0.015
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 202 tttaaaatttaaaattta 219
           ||||||||||||||||||
Sbjct: 664 tttaaaatttaaaattta 647


 Score = 28.2 bits (14), Expect = 3.6
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 202 tttaaaatttaaaa 215
           ||||||||||||||
Sbjct: 657 tttaaaatttaaaa 644


>Contig-U05084-1 (Contig-U05084-1Q) /CSM_Contig/Contig-U05084-1Q.Seq.d
          Length = 828

 Score = 36.2 bits (18), Expect = 0.015
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 202 tttaaaatttaaaattta 219
           ||||||||||||||||||
Sbjct: 763 tttaaaatttaaaattta 780


 Score = 30.2 bits (15), Expect = 0.90
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 205 aaaatttaaaattta 219
           |||||||||||||||
Sbjct: 759 aaaatttaaaattta 773


 Score = 28.2 bits (14), Expect = 3.6
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 202 tttaaaatttaaaa 215
           ||||||||||||||
Sbjct: 770 tttaaaatttaaaa 783


  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: 3119
Number of Sequences: 6905
Number of extensions: 3119
Number of successful extensions: 1139
Number of sequences better than 10.0: 146
length of query: 219
length of database: 5,674,871
effective HSP length: 15
effective length of query: 204
effective length of database: 5,571,296
effective search space: 1136544384
effective search space used: 1136544384
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. 6.23
Homology vs DNA 
Query= Contig-U04544-1 (Contig-U04544-1Q) /CSM_Contig/Contig-U04544-1Q.Seq.d
         (219 letters)

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

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

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

(AU071384) Dictyostelium discoideum slug cDNA, clone SSB374.      141   1e-31  2
(CR788324) Zebrafish DNA sequence from clone DKEY-264B7 in l...    46   0.52   1
(CR450696) Zebrafish DNA sequence from clone CH211-147K9 in ...    46   0.52   1
(EA380746) Sequence 29569 from patent US 7314974.                  44   2.1    1
(Z35640) Caenorhabditis elegans Cosmid F43D9.                      44   2.1    1
(ER450657) 1092963848379 Global-Ocean-Sampling_GS-35-01-01-1...    44   2.1    1
(CU575212) Theobroma cacao, mRNA sequence (KZ0AAP1YH23).           44   2.1    1
(AC165503) Bos taurus clone CH240-176E12, WORKING DRAFT SEQU...    42   3.8    3
(AC118786) Rattus norvegicus clone CH230-364N10, WORKING DRA...    34   3.8    2
(AC118873) Rattus norvegicus clone CH230-486G1, *** SEQUENCI...    34   3.8    2
(AC129686) Rattus norvegicus clone CH230-118B12, *** SEQUENC...    32   3.8    2
(AC133689) Rattus norvegicus clone CH230-211B12, *** SEQUENC...    34   3.9    2
(CV585620) L_AI-aaa18f03.g1 Hc7B_Y Ajellomyces capsulatus cD...    32   5.4    2
(AM440207) Vitis vinifera contig VV78X007893.11, whole genom...    42   8.1    1
(AL132862) Caenorhabditis elegans YAC Y73F8A.                      42   8.1    1
(AL449264) Human DNA sequence from clone RP11-485H8 on chrom...    42   8.1    1
(ER543598) 1093016094665 Global-Ocean-Sampling_GS-35-01-01-1...    42   8.1    1
(EK031570) 1092955413686 Global-Ocean-Sampling_GS-31-01-01-1...    42   8.1    1
(CW951987) TcB37.3_E12_T7 Tribolium BAC library Tribolium ca...    42   8.1    1
(CU793466) A BAC library has been constructed from PN40024 g...    42   8.1    1
(CT551517) A BAC library has been constructed from cultivar ...    42   8.1    1
(CU608535) Theobroma cacao, mRNA sequence (KZ0AAM4YK09FM1).        42   8.1    1
(FG666317) G1142P312RJ12.T0 Anolis carolinensis pooled norma...    42   8.1    1
(AC148352) Sorex araneus clone SA_Ba-162J7, WORKING DRAFT SE...    38   9.3    2

>(AU071384) Dictyostelium discoideum slug cDNA, clone SSB374.
          Length = 220

 Score =  141 bits (71), Expect(2) = 1e-31
 Identities = 77/77 (100%)
 Strand = Plus / Plus


Query: 82  caaagttgtaatttttcaataaaagatancttaaaagggaaaaattgagattgaagcaag 141
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 82  caaagttgtaatttttcaataaaagatancttaaaagggaaaaattgagattgaagcaag 141


Query: 142 attanatatactgagac 158
           |||||||||||||||||
Sbjct: 142 attanatatactgagac 158

 Score = 28.2 bits (14), Expect(2) = 1e-31
 Identities = 14/14 (100%)
 Strand = Plus / Plus


Query: 1  taattaattaattt 14
          ||||||||||||||
Sbjct: 1  taattaattaattt 14

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 116,078,546
Number of extensions: 9342394
Number of successful extensions: 2994062
Number of sequences better than 10.0: 24
Length of query: 219
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 196
Effective length of database: 99,442,330,388
Effective search space: 19490696756048
Effective search space used: 19490696756048
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04544-1 (Contig-U04544-1Q) /CSM_Contig/Contig-U04544-1Q.Seq.d
         (219 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: 38,900,921
Number of extensions: 158580
Number of successful extensions: 120
Number of sequences better than 10.0: 0
Number of HSP's gapped: 120
Number of HSP's successfully gapped: 0
Length of query: 73
Length of database: 1,061,185,681
Length adjustment: 44
Effective length of query: 29
Effective length of database: 917,373,969
Effective search space: 26603845101
Effective search space used: 26603845101
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: 27 (15.0 bits)
PSORT 

 psg: 0.32  gvh: 0.12  alm: 0.81  top: 0.53  tms: 0.00  mit: 0.22  mip: 0.00
 nuc: 0.59  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 

	 68.0 %: nuclear
	 20.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U04544-1 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