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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-U09503-1
Contig ID Contig-U09503-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U09503-1 (Contig-U09503-1Q) /CSM_Contig/Contig-U09503-1Q.Seq.d
ATTCAATTTTAATACATATATATATATATACACACACACATCACATGATC
ACTTTTTTTTTTTTCTCACTCTTTGTATACAAACAATTATTTTTTTTATA
AATATTTTAATTTATTATTATTATTTTTAATTTAATAATGAAAAGTCAAT
CTTTAATAATTTACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAT----------GGGNCCCNTTCCCCCNTTTNNCGNTTGNTTTTTGG
GGGTTGGGGGTCCTTACCCCCCCGTTTTGGGGGGGTTTCCCCCGCCCCCC
CCCTGGGGGTTTTCGGGGGTTNGGCCCCCCCTCCCCCCNTCTTATNTGCT
TGCCNNGTTTTTCCACACTTGACGGGGGGTGGTTCCCCCCTTTTTTTTTA
CCCCCCTTTTTTTTTTTTNTTTTCCCCGTTTGGGTTTCCCCCCCCTCTTT
CGGGTGGGTGGTTTCCTTTTTTTTTCTTTTTTTTTTCCTTTCCTCCCCCC
CCCCCTTTTTTTTGGTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTCCCCTTTTTGGGGGGGGAAAAAAAG
GGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Gap gap included
Contig length 683
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 2
Link to clone list U09503
List of clone(s) 

est1=SSL770F,1,206
est2=SSL770Z,207,685
Translated Amino Acid sequence 
silihiyiyththhmitffffslfvykqlffl*if*FIIIIFNLIMKSQSLIIYQKKKKK
KKKKKKK---

---GXXSPXXRLXFGGWGSLPPRFGGVSPAPPLGVFGGXAPPPPXLXACXVFPHLTGGGS
PLFFYPPFFFXFSPFGFPPPLSGGWFPFFFFFFSFPPPPPFFWFFFFFFFLFFFFFFFFF
FFFPLFGGGKKGEKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
Translated Amino Acid sequence (All Frames) 
Frame A:
iqf*yiyiyihthit*slfffshslytnnyffykyfnllllfli***kvnl**ftkkkkk
kkkkkkkk---

---GXXSPXXRLXFGGWGSLPPRFGGVSPAPPLGVFGGXAPPPPXLXACXVFPHLTGGGS
PLFFYPPFFFXFSPFGFPPPLSGGWFPFFFFFFSFPPPPPFFWFFFFFFFLFFFFFFFFF
FFFPLFGGGKKGEKKKKKKKKKKKKKKKKKKKKKKKKKKKKK

Frame B:
fnfntyiyiythtshdhffffltlciqtiiffiniliyyyyf*fnneksifnnlpkkkkk
kkkkkkkn---

---gpxppfxxxflgvggpyppvlggfpppppwgfsgvxpplppsyxlaxffht*rgvvp
pffftplfffxfprlgfpplfrvggflffsfffpflppplffgfffffffcfffffffff
fffpflggekkgkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk

Frame C:
silihiyiyththhmitffffslfvykqlffl*if*FIIIIFNLIMKSQSLIIYQKKKKK
KKKKKKK---

---xpfpxxxxxfwglgvltppfwggfprpppggfrgxgppspxlxclpxfstldggwfp
pfflppffffxfpvwvsppsfgwvvsffflffflsspppfflvfffffffvfffffffff
ffspfwggkkrgkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U09503-1 (Contig-U09503-1Q)
/CSM_Contig/Contig-U09503-1Q.Seq.d
         (693 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U09503-1 (Contig-U09503-1Q) /CSM_Contig/Conti...   103  2e-22
Contig-U09872-1 (Contig-U09872-1Q) /CSM_Contig/Conti...    42  8e-04
Contig-U09117-1 (Contig-U09117-1Q) /CSM_Contig/Conti...    42  8e-04
Contig-U14068-1 (Contig-U14068-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U12464-1 (Contig-U12464-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U11451-1 (Contig-U11451-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U14303-1 (Contig-U14303-1Q) /CSM_Contig/Conti...    38  0.012
Contig-U13936-1 (Contig-U13936-1Q) /CSM_Contig/Conti...    38  0.012
Contig-U12711-1 (Contig-U12711-1Q) /CSM_Contig/Conti...    38  0.012
Contig-U12257-1 (Contig-U12257-1Q) /CSM_Contig/Conti...    38  0.012

>Contig-U09503-1 (Contig-U09503-1Q) /CSM_Contig/Contig-U09503-1Q.Seq.d
          Length = 693

 Score =  103 bits (52), Expect = 2e-22
 Identities = 52/52 (100%)
 Strand = Plus / Plus

                                                              
Query: 1  attcaattttaatacatatatatatatatacacacacacatcacatgatcac 52
          ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  attcaattttaatacatatatatatatatacacacacacatcacatgatcac 52


 Score = 83.8 bits (42), Expect = 2e-16
 Identities = 42/42 (100%)
 Strand = Plus / Plus

                                                     
Query: 420 ttttccccgtttgggtttcccccccctctttcgggtgggtgg 461
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 420 ttttccccgtttgggtttcccccccctctttcgggtgggtgg 461


 Score = 83.8 bits (42), Expect = 2e-16
 Identities = 51/51 (100%)
 Strand = Plus / Plus

                                                              
Query: 340 tcttatntgcttgccnngtttttccacacttgacggggggtggttcccccc 390
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 340 tcttatntgcttgccnngtttttccacacttgacggggggtggttcccccc 390


 Score = 56.0 bits (28), Expect = 5e-08
 Identities = 28/28 (100%)
 Strand = Plus / Plus

                                       
Query: 576 cccctttttggggggggaaaaaaagggg 603
           ||||||||||||||||||||||||||||
Sbjct: 576 cccctttttggggggggaaaaaaagggg 603


 Score = 54.0 bits (27), Expect = 2e-07
 Identities = 27/27 (100%)
 Strand = Plus / Plus

                                      
Query: 139 tgaaaagtcaatctttaataatttacc 165
           |||||||||||||||||||||||||||
Sbjct: 139 tgaaaagtcaatctttaataatttacc 165


>Contig-U09872-1 (Contig-U09872-1Q) /CSM_Contig/Contig-U09872-1Q.Seq.d
          Length = 1623

 Score = 42.1 bits (21), Expect = 8e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                 
Query: 16   atatatatatatatacacaca 36
            |||||||||||||||||||||
Sbjct: 1568 atatatatatatatacacaca 1588


 Score = 40.1 bits (20), Expect = 0.003
 Identities = 26/28 (92%)
 Strand = Plus / Plus

                                        
Query: 11   aatacatatatatatatatacacacaca 38
            |||| ||||||||||||||| |||||||
Sbjct: 1561 aatatatatatatatatatatacacaca 1588


 Score = 34.2 bits (17), Expect = 0.19
 Identities = 23/25 (92%)
 Strand = Plus / Plus

                                     
Query: 16   atatatatatatatacacacacaca 40
            ||||||||||||||| | |||||||
Sbjct: 1564 atatatatatatatatatacacaca 1588


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                           
Query: 16   atatatatatatata 30
            |||||||||||||||
Sbjct: 1579 atatatatatatata 1565


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                           
Query: 16   atatatatatatata 30
            |||||||||||||||
Sbjct: 1581 atatatatatatata 1567


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                           
Query: 16   atatatatatatata 30
            |||||||||||||||
Sbjct: 1577 atatatatatatata 1563


>Contig-U09117-1 (Contig-U09117-1Q) /CSM_Contig/Contig-U09117-1Q.Seq.d
          Length = 1009

 Score = 42.1 bits (21), Expect = 8e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 10  taatacatatatatatatata 30
           |||||||||||||||||||||
Sbjct: 895 taatacatatatatatatata 915


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 16  atatatatatatata 30
           |||||||||||||||
Sbjct: 873 atatatatatatata 887


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 16  atatatatatatata 30
           |||||||||||||||
Sbjct: 871 atatatatatatata 885


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                          
Query: 16  atatatatatatata 30
           |||||||||||||||
Sbjct: 886 atatatatatatata 872


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 16  atatatatatatata 30
           |||||||||||||||
Sbjct: 903 atatatatatatata 917


 Score = 30.2 bits (15), Expect = 3.0
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                          
Query: 16  atatatatatatata 30
           |||||||||||||||
Sbjct: 916 atatatatatatata 902


  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: 5051
Number of Sequences: 6905
Number of extensions: 5051
Number of successful extensions: 1548
Number of sequences better than 10.0: 174
length of query: 693
length of database: 5,674,871
effective HSP length: 16
effective length of query: 677
effective length of database: 5,564,391
effective search space: 3767092707
effective search space used: 3767092707
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2008.11.16
Homology vs DNA 
Query= Contig-U09503-1 (Contig-U09503-1Q) /CSM_Contig/Contig-U09503-1Q.Seq.d
         (693 letters)

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

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

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

(C93835) Dictyostelium discoideum slug cDNA, clone SSL770.         72   2e-11  2
(AU074757) Dictyostelium discoideum slug cDNA, clone SSL770.       44   8e-11  3

>(C93835) Dictyostelium discoideum slug cDNA, clone SSL770.
          Length = 479

 Score = 71.9 bits (36), Expect(2) = 2e-11
 Identities = 45/45 (100%)
 Strand = Plus / Plus


Query: 340 tcttatntgcttgccnngtttttccacacttgacggggggtggtt 384
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 125 tcttatntgcttgccnngtttttccacacttgacggggggtggtt 169

 Score = 34.2 bits (17), Expect(2) = 2e-11
 Identities = 17/17 (100%)
 Strand = Plus / Plus


Query: 576 cccctttttgggggggg 592
           |||||||||||||||||
Sbjct: 361 cccctttttgggggggg 377

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 128,651,257
Number of extensions: 9322452
Number of successful extensions: 633036
Number of sequences better than 10.0: 2
Length of query: 693
Length of database: 95,242,211,685
Length adjustment: 24
Effective length of query: 669
Effective length of database: 97,308,875,965
Effective search space: 65099638020585
Effective search space used: 65099638020585
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 6.26
Homology vs Protein 
Query= Contig-U09503-1 (Contig-U09503-1Q) /CSM_Contig/Contig-U09503-1Q.Seq.d
         (693 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 337,941,930
Number of extensions: 3056358
Number of successful extensions: 3905
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3883
Number of HSP's successfully gapped: 0
Length of query: 231
Length of database: 1,040,966,779
Length adjustment: 124
Effective length of query: 107
Effective length of database: 643,635,439
Effective search space: 68868991973
Effective search space used: 68868991973
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: 31 (16.5 bits)
PSORT 

 psg: 0.77  gvh: 0.48  alm: 0.16  top: 0.93  tms: 0.13  mit: 0.07  mip: 0.00
 nuc: 3.01  erl: 0.00  erm: 0.80  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: 1.00  m_ : 0.00 

	 60.0 %: nuclear
	 12.0 %: endoplasmic reticulum
	  8.0 %: plasma membrane
	  8.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: mitochondrial

>> prediction for Contig-U09503-1 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