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Dicty_cDB
Contig List | Clone List | cDNA Library List
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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-U01942-1
Contig ID Contig-U01942-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01942-1 (Contig-U01942-1Q) /CSM_Contig/Contig-U01942-1Q.Seq.d
TAAAACCGAAACTGAAATTAATTTTGTAGTTAATTCTCAATGAATGCTGT
ATAATAGAAGAAAAATATGATGATGAAGACTTTACTGGTAATGGTAATAG
TTTTTATAATAATAATATTGTAAATAGTTCGATAAAAATTAATAATAGTA
ATAATAATAGTAATAATAATAATAATCAATGTAAATTCAATATTGGTAGA
AGAAAGATTGTTTCAAGATCAACTTCTCAACCTTCTTTTTATTCAAATAA
AGAATATTCATTTTAATTAAATTTATTTAGAAAAATGAATATATATATTA
ATAAA
Gap no gap
Contig length 305
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 1296493
End point 1296188
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U01942
List of clone(s) 

est1=SSL411Z,1,306
Translated Amino Acid sequence 
kpklklil*LILNECCIIEEKYDDEDFTGNGNSFYNNNIVNSSIKINNSNNNSNNNNNQC
KFNIGRRKIVSRSTSQPSFYSNKEYSF*lnlfrkmniyink
Translated Amino Acid sequence (All Frames) 
Frame A:
*nrn*n*fcs*fsmnav**kknmmmktllvmvivfiiiil*ivr*kliiviiiviiiiin
vnsilveerlfqdqllnllfiqiknihfn*iylek*iyili


Frame B:
kteteinfvvnsq*mlynrrki***rlyw*w**fl***yck*fdkn************sm
*iqyw*kkdcfkinfstfflfk*rifilikfi*kneyiy**


Frame C:
kpklklil*LILNECCIIEEKYDDEDFTGNGNSFYNNNIVNSSIKINNSNNNSNNNNNQC
KFNIGRRKIVSRSTSQPSFYSNKEYSF*lnlfrkmniyink
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U01942-1 (Contig-U01942-1Q)
/CSM_Contig/Contig-U01942-1Q.Seq.d
         (305 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01942-1 (Contig-U01942-1Q) /CSM_Contig/Conti...   224  4e-59
Contig-U02881-1 (Contig-U02881-1Q) /CSM_Contig/Conti...    38  0.005
Contig-U12946-1 (Contig-U12946-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U11229-1 (Contig-U11229-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U06421-1 (Contig-U06421-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U04677-1 (Contig-U04677-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U12494-1 (Contig-U12494-1Q) /CSM_Contig/Conti...    34  0.082
Contig-U12085-1 (Contig-U12085-1Q) /CSM_Contig/Conti...    34  0.082
Contig-U12069-1 (Contig-U12069-1Q) /CSM_Contig/Conti...    34  0.082
Contig-U11931-1 (Contig-U11931-1Q) /CSM_Contig/Conti...    34  0.082

>Contig-U01942-1 (Contig-U01942-1Q) /CSM_Contig/Contig-U01942-1Q.Seq.d
          Length = 305

 Score =  224 bits (113), Expect = 4e-59
 Identities = 113/113 (100%)
 Strand = Plus / Plus

                                                                       
Query: 193 ttggtagaagaaagattgtttcaagatcaacttctcaaccttctttttattcaaataaag 252
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193 ttggtagaagaaagattgtttcaagatcaacttctcaaccttctttttattcaaataaag 252

                                                                
Query: 253 aatattcattttaattaaatttatttagaaaaatgaatatatatattaataaa 305
           |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 253 aatattcattttaattaaatttatttagaaaaatgaatatatatattaataaa 305


 Score =  206 bits (104), Expect = 1e-53
 Identities = 104/104 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   taaaaccgaaactgaaattaattttgtagttaattctcaatgaatgctgtataatagaag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   taaaaccgaaactgaaattaattttgtagttaattctcaatgaatgctgtataatagaag 60

                                                       
Query: 61  aaaaatatgatgatgaagactttactggtaatggtaatagtttt 104
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aaaaatatgatgatgaagactttactggtaatggtaatagtttt 104


>Contig-U02881-1 (Contig-U02881-1Q) /CSM_Contig/Contig-U02881-1Q.Seq.d
          Length = 1290

 Score = 38.2 bits (19), Expect = 0.005
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                  
Query: 57  gaagaaaaatatgatgatgaaga 79
           |||||||| ||||||||||||||
Sbjct: 434 gaagaaaattatgatgatgaaga 456


>Contig-U12946-1 (Contig-U12946-1Q) /CSM_Contig/Contig-U12946-1Q.Seq.d
          Length = 701

 Score = 36.2 bits (18), Expect = 0.021
 Identities = 24/26 (92%)
 Strand = Plus / Plus

                                     
Query: 256 attcattttaattaaatttatttaga 281
           |||||| ||||| |||||||||||||
Sbjct: 215 attcatcttaatcaaatttatttaga 240


  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: 6986
Number of Sequences: 6905
Number of extensions: 6986
Number of successful extensions: 2390
Number of sequences better than 10.0: 276
length of query: 305
length of database: 5,674,871
effective HSP length: 15
effective length of query: 290
effective length of database: 5,571,296
effective search space: 1615675840
effective search space used: 1615675840
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. 5.10
Homology vs DNA 
Query= Contig-U01942-1 (Contig-U01942-1Q) /CSM_Contig/Contig-U01942-1Q.Seq.d
         (305 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

(AU038732) Dictyostelium discoideum slug cDNA, clone SSL411.      172   9e-58  2
(AL353756) Human DNA sequence from clone RP11-415D9 on chrom...    50   0.048  1
(AC181950) Strongylocentrotus purpuratus clone R3-1006P10, W...    46   0.75   1
(AC179610) Strongylocentrotus purpuratus clone R3-1028M04, W...    46   0.75   1
(FG646102) CSRLCD001_05-G10-pAL17d Healthy leaf tissue Solan...    46   0.75   1
(BM579253) 17000687237959 A.Gam.ad.cDNA.blood1 Anopheles gam...    38   2.3    2
(BX322628) Zebrafish DNA sequence from clone CH211-177P17 in...    44   3.0    1
(AM430533) Vitis vinifera contig VV78X226489.11, whole genom...    44   3.0    1
(AE001369) Plasmodium falciparum 3D7 chromosome 2 section 6 ...    44   3.0    1
(AC118364) Rattus norvegicus clone CH230-325H3, *** SEQUENCI...    44   3.0    1
(AC096435) Rattus norvegicus clone CH230-44G5, *** SEQUENCIN...    44   3.0    1
(EK086778) 1092961158900 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.0    1
(EJ519217) 1092955123654 Global-Ocean-Sampling_GS-29-01-01-1...    44   3.0    1
(EJ514900) 1092955078891 Global-Ocean-Sampling_GS-29-01-01-1...    44   3.0    1
(EL496742) G12_PFBAMHI-L-T3-PLATE10A.AB1 Blood stage Plasmod...    44   3.0    1
(EL496469) G06_PFBAMHI-L-T3-PLATE5A.AB1 Blood stage Plasmodi...    44   3.0    1
(EL495984) F08_PFBAMHI-M-T3-PLATE23A.AB1 Blood stage Plasmod...    44   3.0    1
(EL492740) A01_PFBAMHI-M-T3-PLATE27A.AB1 Blood stage Plasmod...    44   3.0    1
(EH995886) AGENCOURT_97631238 NIH_ZGC_10 Danio rerio cDNA cl...    44   3.0    1
(CP000382) Clostridium novyi NT, complete genome.                  44   3.0    1
(AE017321) Wolbachia endosymbiont strain TRS of Brugia malay...    44   3.0    1
(ET350507) S0160F19_SP6 CHORI-214 Salmo salar genomic clone ...    32   7.6    2

>(AU038732) Dictyostelium discoideum slug cDNA, clone SSL411.
          Length = 306

 Score =  172 bits (87), Expect(2) = 9e-58
 Identities = 87/87 (100%)
 Strand = Plus / Plus


Query: 1  taaaaccgaaactgaaattaattttgtagttaattctcaatgaatgctgtataatagaag 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  taaaaccgaaactgaaattaattttgtagttaattctcaatgaatgctgtataatagaag 60


Query: 61 aaaaatatgatgatgaagactttactg 87
          |||||||||||||||||||||||||||
Sbjct: 61 aaaaatatgatgatgaagactttactg 87

 Score = 85.7 bits (43), Expect(2) = 9e-58
 Identities = 43/43 (100%)
 Strand = Plus / Plus


Query: 193 ttggtagaagaaagattgtttcaagatcaacttctcaaccttc 235
           |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193 ttggtagaagaaagattgtttcaagatcaacttctcaaccttc 235

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 195,092,038
Number of extensions: 12822138
Number of successful extensions: 1278616
Number of sequences better than 10.0: 22
Length of query: 305
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 282
Effective length of database: 99,442,330,388
Effective search space: 28042737169416
Effective search space used: 28042737169416
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01942-1 (Contig-U01942-1Q) /CSM_Contig/Contig-U01942-1Q.Seq.d
         (305 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: 222,376,153
Number of extensions: 2560098
Number of successful extensions: 2839
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2839
Number of HSP's successfully gapped: 0
Length of query: 101
Length of database: 1,051,180,864
Length adjustment: 69
Effective length of query: 32
Effective length of database: 827,858,293
Effective search space: 26491465376
Effective search space used: 26491465376
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: 0.75  gvh: 0.08  alm: 0.67  top: 0.53  tms: 0.00  mit: 0.21  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
	 16.0 %: cytoskeletal
	 12.0 %: mitochondrial

>> prediction for Contig-U01942-1 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