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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-U03442-1
Contig ID Contig-U03442-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U03442-1 (Contig-U03442-1Q) /CSM_Contig/Contig-U03442-1Q.Seq.d
GTTNTTTTGGAAAGAGATATGGGGTATTCATACACATGNTACTGTTTTAN
ATAAANAGAGATCNTTGATAATTCCATANTTTAAGNTCTTCCAGATGAGG
ACTGGAATGATGATAGAGTGNCTCAAGTTAGTTNCAGANTCNTGTAAAAT
TTTCTCACAAAAAGGTTATNTTCATAAAGGTGTNCCCTCAGAGACATGTT
GCCTCAATATGCNGNATCTGATAAAATTGAGATAGTATTCATAGATTTAT
GAAGAGTAGAATGAGATTAGTGTAGCCTAGGAGTGAAAGAAA
Gap no gap
Contig length 292
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 U03442
List of clone(s) 

est1=SFC495Z,1,293
Translated Amino Acid sequence 
XFWKEIWGIHTHXTVLXKXRSLIIPXFKXFQMRTGMMIEXLKLVXXSCKIFSQKGYXHKG
VPSETCCLNMXXLIKLR*ys*iyee*neisva*e*kk
Translated Amino Acid sequence (All Frames) 
Frame A:
vxlerdmgysytxycfx*xeixdnsix*xlpdedwnddrvxqvsxrxx*nfltkrlxs*r
cxlrdmlpqyaxsdkieivfidl*rve*d*cslgvke


Frame B:
XFWKEIWGIHTHXTVLXKXRSLIIPXFKXFQMRTGMMIEXLKLVXXSCKIFSQKGYXHKG
VPSETCCLNMXXLIKLR*ys*iyee*neisva*e*kk


Frame C:
xfgkrygvfihmxlfxixrdx**fhxlxssr*gle***sxss*xqxxvkfshkkvxfikv
xpqrhvasicxi**n*dsihrfmksrmrlv*prser
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U03442-1 (Contig-U03442-1Q)
/CSM_Contig/Contig-U03442-1Q.Seq.d
         (292 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U03442-1 (Contig-U03442-1Q) /CSM_Contig/Conti...   490  e-139
Contig-U12042-1 (Contig-U12042-1Q) /CSM_Contig/Conti...    32  0.31
Contig-U12511-1 (Contig-U12511-1Q) /CSM_Contig/Conti...    30  1.2
Contig-U12447-1 (Contig-U12447-1Q) /CSM_Contig/Conti...    30  1.2
Contig-U11297-1 (Contig-U11297-1Q) /CSM_Contig/Conti...    30  1.2
Contig-U09715-1 (Contig-U09715-1Q) /CSM_Contig/Conti...    30  1.2
Contig-U03300-1 (Contig-U03300-1Q) /CSM_Contig/Conti...    30  1.2
Contig-U14711-1 (Contig-U14711-1Q) /CSM_Contig/Conti...    28  4.8
Contig-U14188-1 (Contig-U14188-1Q) /CSM_Contig/Conti...    28  4.8

>Contig-U03442-1 (Contig-U03442-1Q) /CSM_Contig/Contig-U03442-1Q.Seq.d
          Length = 292

 Score =  490 bits (247), Expect = e-139
 Identities = 292/292 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   gttnttttggaaagagatatggggtattcatacacatgntactgttttanataaanagag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gttnttttggaaagagatatggggtattcatacacatgntactgttttanataaanagag 60

                                                                       
Query: 61  atcnttgataattccatantttaagntcttccagatgaggactggaatgatgatagagtg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  atcnttgataattccatantttaagntcttccagatgaggactggaatgatgatagagtg 120

                                                                       
Query: 121 nctcaagttagttncagantcntgtaaaattttctcacaaaaaggttatnttcataaagg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 nctcaagttagttncagantcntgtaaaattttctcacaaaaaggttatnttcataaagg 180

                                                                       
Query: 181 tgtnccctcagagacatgttgcctcaatatgcngnatctgataaaattgagatagtattc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tgtnccctcagagacatgttgcctcaatatgcngnatctgataaaattgagatagtattc 240

                                                               
Query: 241 atagatttatgaagagtagaatgagattagtgtagcctaggagtgaaagaaa 292
           ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 atagatttatgaagagtagaatgagattagtgtagcctaggagtgaaagaaa 292


>Contig-U12042-1 (Contig-U12042-1Q) /CSM_Contig/Contig-U12042-1Q.Seq.d
          Length = 1435

 Score = 32.2 bits (16), Expect = 0.31
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                            
Query: 252  aagagtagaatgagat 267
            ||||||||||||||||
Sbjct: 1082 aagagtagaatgagat 1067


>Contig-U12511-1 (Contig-U12511-1Q) /CSM_Contig/Contig-U12511-1Q.Seq.d
          Length = 952

 Score = 30.2 bits (15), Expect = 1.2
 Identities = 18/19 (94%)
 Strand = Plus / Plus

                              
Query: 229 gagatagtattcatagatt 247
           |||||| ||||||||||||
Sbjct: 583 gagatattattcatagatt 601


  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: 1006
Number of Sequences: 6905
Number of extensions: 1006
Number of successful extensions: 258
Number of sequences better than 10.0: 19
length of query: 292
length of database: 5,674,871
effective HSP length: 15
effective length of query: 277
effective length of database: 5,571,296
effective search space: 1543248992
effective search space used: 1543248992
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. 5.31
Homology vs DNA 
Query= Contig-U03442-1 (Contig-U03442-1Q) /CSM_Contig/Contig-U03442-1Q.Seq.d
         (292 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

(BJ399425) Dictyostelium discoideum cDNA clone:dds5n24, 3' e...   490   e-134  1
(CR626944) Zebrafish DNA sequence from clone DKEY-103M22 in ...    42   7.4    2
(AC171496) Bos taurus clone CH240-262I23, WORKING DRAFT SEQU...    42   9.3    3

>(BJ399425) Dictyostelium discoideum cDNA clone:dds5n24, 3' end,
           single read.
          Length = 293

 Score =  490 bits (247), Expect = e-134
 Identities = 292/292 (100%)
 Strand = Plus / Minus


Query: 1   gttnttttggaaagagatatggggtattcatacacatgntactgttttanataaanagag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 293 gttnttttggaaagagatatggggtattcatacacatgntactgttttanataaanagag 234


Query: 61  atcnttgataattccatantttaagntcttccagatgaggactggaatgatgatagagtg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 233 atcnttgataattccatantttaagntcttccagatgaggactggaatgatgatagagtg 174


Query: 121 nctcaagttagttncagantcntgtaaaattttctcacaaaaaggttatnttcataaagg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 173 nctcaagttagttncagantcntgtaaaattttctcacaaaaaggttatnttcataaagg 114


Query: 181 tgtnccctcagagacatgttgcctcaatatgcngnatctgataaaattgagatagtattc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 113 tgtnccctcagagacatgttgcctcaatatgcngnatctgataaaattgagatagtattc 54


Query: 241 atagatttatgaagagtagaatgagattagtgtagcctaggagtgaaagaaa 292
           ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 53  atagatttatgaagagtagaatgagattagtgtagcctaggagtgaaagaaa 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 229,812,984
Number of extensions: 12183234
Number of successful extensions: 694861
Number of sequences better than 10.0: 3
Length of query: 292
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 269
Effective length of database: 99,442,330,388
Effective search space: 26749986874372
Effective search space used: 26749986874372
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.28
Homology vs Protein 
Query= Contig-U03442-1 (Contig-U03442-1Q) /CSM_Contig/Contig-U03442-1Q.Seq.d
         (292 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: 332,728,680
Number of extensions: 4328095
Number of successful extensions: 2713
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2712
Number of HSP's successfully gapped: 0
Length of query: 97
Length of database: 1,061,185,681
Length adjustment: 66
Effective length of query: 31
Effective length of database: 845,468,113
Effective search space: 26209511503
Effective search space used: 26209511503
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: 28 (15.4 bits)
PSORT 

 psg: 0.80  gvh: 0.57  alm: 0.46  top: 0.53  tms: 0.00  mit: 0.31  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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
	 20.0 %: mitochondrial
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for Contig-U03442-1 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) 0
SH (FL, L) 0
SF (FL, S) 1
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0