NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U14834-1
Contig ID Contig-U14834-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14834-1 (Contig-U14834-1Q) /CSM_Contig/Contig-U14834-1Q.Seq.d
ATGAAAAGAAACCACCAATTGGAACTATTCATGTCCTTAAATCTGATTTT
TTACCAATGTTAAGATAAAAATAAAAATAAAAATATAAAGTAAAACAATT
TTTATATGTAAAAAAAAAA
Gap no gap
Contig length 119
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 711570
End point 711464
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U14834
List of clone(s) 

est1=VHJ883Z,1,106
est2=VHJ883F,16,119
Translated Amino Acid sequence 
EKKPPIGTIHVLKSDFLPMLR*k*k*kykvkqflyvkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
mkrnhqlelfmslnlifyqc*dknknknik*nnfym*kk


Frame B:
*kettnwnyscp*i*fftnvkikikiki*sktifickkk


Frame C:
EKKPPIGTIHVLKSDFLPMLR*k*k*kykvkqflyvkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14834-1 (Contig-U14834-1Q)
/CSM_Contig/Contig-U14834-1Q.Seq.d
         (119 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14834-1 (Contig-U14834-1Q) /CSM_Contig/Conti...   127  3e-30
Contig-U12387-1 (Contig-U12387-1Q) /CSM_Contig/Conti...    32  0.12
Contig-U09534-1 (Contig-U09534-1Q) /CSM_Contig/Conti...    32  0.12
Contig-U05215-1 (Contig-U05215-1Q) /CSM_Contig/Conti...    32  0.12
Contig-U12868-1 (Contig-U12868-1Q) /CSM_Contig/Conti...    30  0.47
Contig-U10495-1 (Contig-U10495-1Q) /CSM_Contig/Conti...    30  0.47
Contig-U14471-1 (Contig-U14471-1Q) /CSM_Contig/Conti...    28  1.8
Contig-U12780-1 (Contig-U12780-1Q) /CSM_Contig/Conti...    28  1.8
Contig-U12493-1 (Contig-U12493-1Q) /CSM_Contig/Conti...    28  1.8
Contig-U12305-1 (Contig-U12305-1Q) /CSM_Contig/Conti...    28  1.8

>Contig-U14834-1 (Contig-U14834-1Q) /CSM_Contig/Contig-U14834-1Q.Seq.d
          Length = 119

 Score =  127 bits (64), Expect = 3e-30
 Identities = 64/64 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  atgaaaagaaaccaccaattggaactattcatgtccttaaatctgattttttaccaatgt 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atgaaaagaaaccaccaattggaactattcatgtccttaaatctgattttttaccaatgt 60

              
Query: 61 taag 64
          ||||
Sbjct: 61 taag 64


>Contig-U12387-1 (Contig-U12387-1Q) /CSM_Contig/Contig-U12387-1Q.Seq.d
          Length = 1449

 Score = 32.2 bits (16), Expect = 0.12
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                            
Query: 4    aaaagaaaccaccaat 19
            ||||||||||||||||
Sbjct: 1170 aaaagaaaccaccaat 1155


>Contig-U09534-1 (Contig-U09534-1Q) /CSM_Contig/Contig-U09534-1Q.Seq.d
          Length = 1411

 Score = 32.2 bits (16), Expect = 0.12
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                               
Query: 39  aaatctgattttttaccaat 58
           |||| |||||||||||||||
Sbjct: 423 aaatttgattttttaccaat 442


  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: 889
Number of Sequences: 6905
Number of extensions: 889
Number of successful extensions: 252
Number of sequences better than 10.0: 88
length of query: 119
length of database: 5,674,871
effective HSP length: 14
effective length of query: 105
effective length of database: 5,578,201
effective search space: 585711105
effective search space used: 585711105
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 2009. 1. 3
Homology vs DNA 
Query= Contig-U14834-1 (Contig-U14834-1Q) /CSM_Contig/Contig-U14834-1Q.Seq.d
         (119 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

(AC117072) Dictyostelium discoideum chromosome 2 map 3879572...   127   8e-26  1
(BJ442734) Dictyostelium discoideum cDNA clone:ddv50f22, 3' ...   127   8e-26  1
(BJ423915) Dictyostelium discoideum cDNA clone:ddv50f22, 5' ...    98   7e-17  1
(AC200011) Ateles geoffroyi clone UC1-30L16, WORKING DRAFT S...    42   3.8    1
(AC177640) Strongylocentrotus purpuratus clone R3-1020F19, W...    42   3.8    1
(EV053701) BNSCS3CT_UP_213_C01_13MAY2007_011 Brassica napus ...    42   3.8    1
(BM959496) PLATE_13_G09_13.AB1 GS Lambda-Triplex, 10 day ger...    42   3.8    1

>(AC117072) Dictyostelium discoideum chromosome 2 map 3879572-4071762
             strain AX4, complete sequence.
          Length = 192187

 Score =  127 bits (64), Expect = 8e-26
 Identities = 64/64 (100%)
 Strand = Plus / Minus


Query: 1     atgaaaagaaaccaccaattggaactattcatgtccttaaatctgattttttaccaatgt 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 23407 atgaaaagaaaccaccaattggaactattcatgtccttaaatctgattttttaccaatgt 23348


Query: 61    taag 64
             ||||
Sbjct: 23347 taag 23344

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 81,155,542
Number of extensions: 4370732
Number of successful extensions: 1109498
Number of sequences better than 10.0: 8
Length of query: 119
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 97
Effective length of database: 93,199,600,587
Effective search space: 9040361256939
Effective search space used: 9040361256939
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7.12
Homology vs Protein 
Query= Contig-U14834-1 (Contig-U14834-1Q) /CSM_Contig/Contig-U14834-1Q.Seq.d
         (119 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC117072_7(AC117072|pid:none) Dictyostelium discoideum chromosom...    47   2e-04

>AC117072_7(AC117072|pid:none) Dictyostelium discoideum chromosome 2
           map 3879572-4071762 strain AX4, complete sequence.
          Length = 131

 Score = 47.0 bits (110), Expect = 2e-04
 Identities = 21/21 (100%), Positives = 21/21 (100%)
 Frame = +3

Query: 3   EKKPPIGTIHVLKSDFLPMLR 65
           EKKPPIGTIHVLKSDFLPMLR
Sbjct: 111 EKKPPIGTIHVLKSDFLPMLR 131

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: 117,163,007
Number of extensions: 1225645
Number of successful extensions: 744
Number of sequences better than 10.0: 1
Number of HSP's gapped: 744
Number of HSP's successfully gapped: 1
Length of query: 39
Length of database: 1,051,180,864
Length adjustment: 13
Effective length of query: 26
Effective length of database: 1,009,105,597
Effective search space: 26236745522
Effective search space used: 26236745522
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: 0.86  gvh: 0.11  alm: 0.49  top: 0.50  tms: 0.00  mit: 0.22  mip: 0.00
 nuc: 0.00  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: 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 %: nuclear
	 32.0 %: cytoplasmic
	 12.0 %: mitochondrial
	  8.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: Golgi

>> prediction for Contig-U14834-1 is nuc
VS (DIR, S) 0
VH (FL, L) 1
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
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