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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-U15423-1
Contig ID Contig-U15423-1
Contig update 2004. 6.11
Contig sequence 
>Contig-U15423-1 (Contig-U15423-1Q) /CSM_Contig/Contig-U15423-1Q.Seq.d
AAAATTAAAAGAAGAAAAAGAAGCTATTAAAGAAAAAGAAGAACAAGAAA
AGATTGAACGTGAGAAACAACGTGAACAACGTCGTATTGAGAAAGAACAA
CGTGAAAAAGAAGAGAGAGAACAAGAGGAGCTCGCTGAAATTGAACGTGA
GAAACAACGTGAACAACGTCGTTTAGAATTAGAACAAGAAGCTAATAAAC
TTGAAGAAGAACGTAAGAAAAGACAAGAAGAAAGAAGACTTCGCAAGAGA
ACAAAAAGAAAGAGAATTGGAAGAAGAAACAAAAAGACTTGAACAAGAAA
GAGAAGAACGTCGTAGAAAGAGAGAAGAAGCTTAAAAATTCTTAAATCTC
ATTTCTTATTAATTTTTAAAAAAAAAAATCCAAAAAAAAAAAAAAGATCC
Gap no gap
Contig length 400
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 3471026
End point 3470623
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U15423
List of clone(s) 

est1=SLF288Z,1,400
Translated Amino Acid sequence 
KLKEEKEAIKEKEEQEKIEREKQREQRRIEKEQREKEEREQEELAEIEREKQREQRRLEL
EQEANKLEEERKKRQEERRLRKRTKRKRIGRRNKKT*trkrrts*kerrslkilkshfll
ifkkknpkkkkrs
Translated Amino Acid sequence (All Frames) 
Frame A:
kikrrkrsy*rkrrtrkd*t*ett*ttsy*ertt*krrertrgar*n*t*ett*ttsfri
rtrs**t*rrt*ektrrkktsqenkkkenwkkkqkdlnkkeknvverekklkns*isfli
nf*kkkskkkkki


Frame B:
KLKEEKEAIKEKEEQEKIEREKQREQRRIEKEQREKEEREQEELAEIEREKQREQRRLEL
EQEANKLEEERKKRQEERRLRKRTKRKRIGRRNKKT*trkrrts*kerrslkilkshfll
ifkkknpkkkkrs


Frame C:
n*kkkkkllkkkknkkrlnvrnnvnnvvlrknnvkkkrenkrsslklnvrnnvnnvv*n*
nkklinlkknvrkdkkkedfareqkereleeetkrleqereerrrkreea*kflnlisy*
flkkkiqkkkkd
own update 2004. 6.23
Homology vs CSM-cDNA 
Query= Contig-U15423-1 (Contig-U15423-1Q)
/CSM_Contig/Contig-U15423-1Q.Seq.d
         (400 letters)

Database: CSM
           8402 sequences; 8,075,542 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U15423-1 (Contig-U15423-1Q) /CSM_Contig/Conti...   293  1e-79
Contig-U10985-1 (Contig-U10985-1Q) /CSM_Contig/Conti...   236  2e-62
Contig-U02361-1 (Contig-U02361-1Q) /CSM_Contig/Conti...    46  4e-05
Contig-U15507-1 (Contig-U15507-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U13319-1 (Contig-U13319-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U15943-1 (Contig-U15943-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U12161-1 (Contig-U12161-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U16523-1 (Contig-U16523-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U16279-1 (Contig-U16279-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U15629-1 (Contig-U15629-1Q) /CSM_Contig/Conti...    34  0.16

>Contig-U15423-1 (Contig-U15423-1Q) /CSM_Contig/Contig-U15423-1Q.Seq.d
          Length = 400

 Score =  293 bits (148), Expect = 1e-79
 Identities = 148/148 (100%)
 Strand = Plus / Plus

                                                                       
Query: 54  ttgaacgtgagaaacaacgtgaacaacgtcgtattgagaaagaacaacgtgaaaaagaag 113
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 54  ttgaacgtgagaaacaacgtgaacaacgtcgtattgagaaagaacaacgtgaaaaagaag 113

                                                                       
Query: 114 agagagaacaagaggagctcgctgaaattgaacgtgagaaacaacgtgaacaacgtcgtt 173
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 114 agagagaacaagaggagctcgctgaaattgaacgtgagaaacaacgtgaacaacgtcgtt 173

                                       
Query: 174 tagaattagaacaagaagctaataaact 201
           ||||||||||||||||||||||||||||
Sbjct: 174 tagaattagaacaagaagctaataaact 201


 Score = 73.8 bits (37), Expect = 2e-13
 Identities = 37/37 (100%)
 Strand = Plus / Plus

                                                
Query: 331 cttaaaaattcttaaatctcatttcttattaattttt 367
           |||||||||||||||||||||||||||||||||||||
Sbjct: 331 cttaaaaattcttaaatctcatttcttattaattttt 367


 Score = 65.9 bits (33), Expect = 4e-11
 Identities = 33/33 (100%)
 Strand = Plus / Plus

                                            
Query: 140 attgaacgtgagaaacaacgtgaacaacgtcgt 172
           |||||||||||||||||||||||||||||||||
Sbjct: 53  attgaacgtgagaaacaacgtgaacaacgtcgt 85


>Contig-U10985-1 (Contig-U10985-1Q) /CSM_Contig/Contig-U10985-1Q.Seq.d
          Length = 4897

 Score =  236 bits (119), Expect = 2e-62
 Identities = 119/119 (100%)
 Strand = Plus / Plus

                                                                        
Query: 54   ttgaacgtgagaaacaacgtgaacaacgtcgtattgagaaagaacaacgtgaaaaagaag 113
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 3920 ttgaacgtgagaaacaacgtgaacaacgtcgtattgagaaagaacaacgtgaaaaagaag 3979

                                                                       
Query: 114  agagagaacaagaggagctcgctgaaattgaacgtgagaaacaacgtgaacaacgtcgt 172
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 3980 agagagaacaagaggagctcgctgaaattgaacgtgagaaacaacgtgaacaacgtcgt 4038


 Score = 93.7 bits (47), Expect = 2e-19
 Identities = 53/55 (96%)
 Strand = Plus / Plus

                                                                   
Query: 54   ttgaacgtgagaaacaacgtgaacaacgtcgtattgagaaagaacaacgtgaaaa 108
            |||||||||||||||||||||||||||||||| | ||||||||||||||||||||
Sbjct: 4007 ttgaacgtgagaaacaacgtgaacaacgtcgtctcgagaaagaacaacgtgaaaa 4061


 Score = 87.7 bits (44), Expect = 1e-17
 Identities = 44/44 (100%)
 Strand = Plus / Plus

                                                        
Query: 158  cgtgaacaacgtcgtttagaattagaacaagaagctaataaact 201
            ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4673 cgtgaacaacgtcgtttagaattagaacaagaagctaataaact 4716


 Score = 69.9 bits (35), Expect = 3e-12
 Identities = 35/35 (100%)
 Strand = Plus / Plus

                                               
Query: 333  taaaaattcttaaatctcatttcttattaattttt 367
            |||||||||||||||||||||||||||||||||||
Sbjct: 4846 taaaaattcttaaatctcatttcttattaattttt 4880


 Score = 65.9 bits (33), Expect = 4e-11
 Identities = 33/33 (100%)
 Strand = Plus / Plus

                                             
Query: 140  attgaacgtgagaaacaacgtgaacaacgtcgt 172
            |||||||||||||||||||||||||||||||||
Sbjct: 3919 attgaacgtgagaaacaacgtgaacaacgtcgt 3951


 Score = 36.2 bits (18), Expect = 0.039
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                  
Query: 69   aacgtgaacaacgtcgtattga 90
            ||||||||||||||||| ||||
Sbjct: 4229 aacgtgaacaacgtcgtcttga 4250


 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 156  aacgtgaacaacgtcgt 172
            |||||||||||||||||
Sbjct: 4229 aacgtgaacaacgtcgt 4245


 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 151 gaaacaacgtgaacaac 167
           |||||||||||||||||
Sbjct: 835 gaaacaacgtgaacaac 851


 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 64  gaaacaacgtgaacaac 80
           |||||||||||||||||
Sbjct: 835 gaaacaacgtgaacaac 851


 Score = 32.2 bits (16), Expect = 0.61
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                            
Query: 136  tgaaattgaacgtgag 151
            ||||||||||||||||
Sbjct: 4263 tgaaattgaacgtgag 4278


 Score = 30.2 bits (15), Expect = 2.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                           
Query: 71   cgtgaacaacgtcgt 85
            |||||||||||||||
Sbjct: 4673 cgtgaacaacgtcgt 4687


>Contig-U02361-1 (Contig-U02361-1Q) /CSM_Contig/Contig-U02361-1Q.Seq.d
          Length = 1258

 Score = 46.1 bits (23), Expect = 4e-05
 Identities = 26/27 (96%)
 Strand = Plus / Plus

                                      
Query: 164 caacgtcgtttagaattagaacaagaa 190
           ||||||||||||||||| |||||||||
Sbjct: 723 caacgtcgtttagaatttgaacaagaa 749


  Database: CSM
    Posted date:  Jun 21, 2004  1:35 PM
  Number of letters in database: 8,075,542
  Number of sequences in database:  8402
  
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: 2896
Number of Sequences: 8402
Number of extensions: 2896
Number of successful extensions: 290
Number of sequences better than 10.0: 83
length of query: 400
length of database: 8,075,542
effective HSP length: 16
effective length of query: 384
effective length of database: 7,941,110
effective search space: 3049386240
effective search space used: 3049386240
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. 1.25
Homology vs DNA 
Query= Contig-U15423-1 (Contig-U15423-1Q) /CSM_Contig/Contig-U15423-1Q.Seq.d
         (400 letters)

Database: ddbj_B
           98,226,423 sequences; 98,766,808,389 total letters

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

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

(AU052898) Dictyostelium discoideum slug cDNA, clone SLF288.       96   5e-26  2
(AU053233) Dictyostelium discoideum slug cDNA, clone SLI189.       92   2e-14  1
(AU034895) Dictyostelium discoideum slug cDNA, clone SLE655.       92   2e-14  1
(BJ340927) Dictyostelium discoideum cDNA clone:dda4n09, 3' e...    92   2e-14  1
(AU039941) Dictyostelium discoideum slug cDNA, clone SLG793.       58   4e-11  3
(AU054170) Dictyostelium discoideum slug cDNA, clone SLK853.       80   7e-11  1
(AU034917) Dictyostelium discoideum slug cDNA, clone SLE688.       50   1e-08  3
(AU054017) Dictyostelium discoideum slug cDNA, clone SLK426.       58   8e-08  2
(AU039251) Dictyostelium discoideum slug cDNA, clone SLH282.       58   9e-08  2
(AU062030) Dictyostelium discoideum slug cDNA, clone SLH282.       56   0.001  1
(BJ344713) Dictyostelium discoideum cDNA clone:dda20c09, 3' ...    34   4.2    2

>(AU052898) Dictyostelium discoideum slug cDNA, clone SLF288.
          Length = 400

 Score = 95.6 bits (48), Expect(2) = 5e-26
 Identities = 48/48 (100%)
 Strand = Plus / Plus


Query: 127 ggagctcgctgaaattgaacgtgagaaacaacgtgaacaacgtcgttt 174
           ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 127 ggagctcgctgaaattgaacgtgagaaacaacgtgaacaacgtcgttt 174

 Score = 58.0 bits (29), Expect(2) = 5e-26
 Identities = 29/29 (100%)
 Strand = Plus / Plus


Query: 339 ttcttaaatctcatttcttattaattttt 367
           |||||||||||||||||||||||||||||
Sbjct: 339 ttcttaaatctcatttcttattaattttt 367

 Score = 65.9 bits (33), Expect = 1e-06
 Identities = 33/33 (100%)
 Strand = Plus / Plus


Query: 140 attgaacgtgagaaacaacgtgaacaacgtcgt 172
           |||||||||||||||||||||||||||||||||
Sbjct: 53  attgaacgtgagaaacaacgtgaacaacgtcgt 85

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 98226423
Number of Hits to DB: 77,129,268
Number of extensions: 4455359
Number of successful extensions: 273163
Number of sequences better than 10.0: 11
Length of query: 400
Length of database: 98,766,808,389
Length adjustment: 23
Effective length of query: 377
Effective length of database: 96,507,600,660
Effective search space: 36383365448820
Effective search space used: 36383365448820
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.16
Homology vs Protein 
Query= Contig-U15423-1 (Contig-U15423-1Q) /CSM_Contig/Contig-U15423-1Q.Seq.d
         (400 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: 49,668,251
Number of extensions: 123956
Number of successful extensions: 107
Number of sequences better than 10.0: 0
Number of HSP's gapped: 107
Number of HSP's successfully gapped: 0
Length of query: 133
Length of database: 1,051,180,864
Length adjustment: 98
Effective length of query: 35
Effective length of database: 733,998,082
Effective search space: 25689932870
Effective search space used: 25689932870
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: 0.22  gvh: -0.16  alm: 0.87  top: 0.53  tms: 0.00  mit: 0.20  mip: 0.00
 nuc: 0.64  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 

	 64.0 %: nuclear
	 24.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U15423-1 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) 1
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