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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-U02018-1
Contig ID Contig-U02018-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U02018-1 (Contig-U02018-1Q) /CSM_Contig/Contig-U02018-1Q.Seq.d
TAATAATAATAATAATAATAATAGTAAAGAAATATTAGAAAGAGAGAAAT
TAAAATTTAAAAATTTTAAAACAAATTATAAAATTGAAAGATTTAGACAA
GTATTACCAGGTTGGGAAATTAGAAGATTTGAAGATAAGAAAAAGAAATT
CATTTTTGTAGCGCCTAATGGTGACGAAAAATGTTATTATCTTAAACATG
CATTACAATGGAATAAAAATAATAAATATGGCGAAAAAATTAAAGACGTT
GAATCATTCTTAATAAATTTTAATAAAGATGTAAAAAAACAAATATCAGA
TAAACGTAAAGAATATGACGATGTTAAAAAAATTGAAAAAAGAAAATTAC
AAAAAGAAGAGGCATTGGAAAAAGAATCTTTAAAATTAAGGGAAAAGGAA
GAATCATCTTTAATTACTAGTAGTAATACTAGTAGAAAAAAAAAAAGATT
AAATTAAAAAATTTTATAAATAATAAAAATATTATTAAATATAAAAAA
Gap no gap
Contig length 498
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 1984285
End point 1984783
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U02018
List of clone(s) 

est1=SSM694Z,1,499
Translated Amino Acid sequence 
NNNNNNNSKEILEREKLKFKNFKTNYKIERFRQVLPGWEIRRFEDKKKKFIFVAPNGDEK
CYYLKHALQWNKNNKYGEKIKDVESFLINFNKDVKKQISDKRKEYDDVKKIEKRKLQKEE
ALEKESLKLREKEESSLITSSNTSRKKKRLN*kil*iikillnik
Translated Amino Acid sequence (All Frames) 
Frame A:
*********rnirkreiki*kf*nkl*n*ki*tsitrlgn*ki*r*ekeihfcsa*w*rk
mlls*tcitme*k**iwrkn*rr*iilnkf**rckktnir*t*ri*rc*kn*kkkitkrr
gigkrifkikgkgriifny***y**kkkkiklknfinnkniikykk


Frame B:
NNNNNNNSKEILEREKLKFKNFKTNYKIERFRQVLPGWEIRRFEDKKKKFIFVAPNGDEK
CYYLKHALQWNKNNKYGEKIKDVESFLINFNKDVKKQISDKRKEYDDVKKIEKRKLQKEE
ALEKESLKLREKEESSLITSSNTSRKKKRLN*kil*iikillnik


Frame C:
iiiiiiivkky*kern*nlkilkqiiklkdldkyyqvgkledlkirkrnsfl*rlmvtkn
viilnmhyngikiinmakklktlnhs**ilikm*knkyqinvknmtmlkklkkenykkkr
hwkknl*n*gkrknhl*llvvilvekkkd*ikkfyk**kyy*i*k
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U02018-1 (Contig-U02018-1Q)
/CSM_Contig/Contig-U02018-1Q.Seq.d
         (498 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U02018-1 (Contig-U02018-1Q) /CSM_Contig/Conti...   387  e-108
Contig-U12590-1 (Contig-U12590-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U12323-1 (Contig-U12323-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U10892-1 (Contig-U10892-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U01854-1 (Contig-U01854-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U00509-1 (Contig-U00509-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U12701-1 (Contig-U12701-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U12507-1 (Contig-U12507-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U12417-1 (Contig-U12417-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U12982-1 (Contig-U12982-1Q) /CSM_Contig/Conti...    28  8.4

>Contig-U02018-1 (Contig-U02018-1Q) /CSM_Contig/Contig-U02018-1Q.Seq.d
          Length = 498

 Score =  387 bits (195), Expect = e-108
 Identities = 195/195 (100%)
 Strand = Plus / Plus

                                                                       
Query: 86  gaaagatttagacaagtattaccaggttgggaaattagaagatttgaagataagaaaaag 145
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86  gaaagatttagacaagtattaccaggttgggaaattagaagatttgaagataagaaaaag 145

                                                                       
Query: 146 aaattcatttttgtagcgcctaatggtgacgaaaaatgttattatcttaaacatgcatta 205
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 146 aaattcatttttgtagcgcctaatggtgacgaaaaatgttattatcttaaacatgcatta 205

                                                                       
Query: 206 caatggaataaaaataataaatatggcgaaaaaattaaagacgttgaatcattcttaata 265
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 206 caatggaataaaaataataaatatggcgaaaaaattaaagacgttgaatcattcttaata 265

                          
Query: 266 aattttaataaagat 280
           |||||||||||||||
Sbjct: 266 aattttaataaagat 280


 Score =  159 bits (80), Expect = 3e-39
 Identities = 80/80 (100%)
 Strand = Plus / Plus

                                                                       
Query: 356 gaagaggcattggaaaaagaatctttaaaattaagggaaaaggaagaatcatctttaatt 415
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 356 gaagaggcattggaaaaagaatctttaaaattaagggaaaaggaagaatcatctttaatt 415

                               
Query: 416 actagtagtaatactagtag 435
           ||||||||||||||||||||
Sbjct: 416 actagtagtaatactagtag 435


>Contig-U12590-1 (Contig-U12590-1Q) /CSM_Contig/Contig-U12590-1Q.Seq.d
          Length = 1074

 Score = 36.2 bits (18), Expect = 0.035
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 260 ttaataaattttaataaa 277
           ||||||||||||||||||
Sbjct: 968 ttaataaattttaataaa 985


>Contig-U12323-1 (Contig-U12323-1Q) /CSM_Contig/Contig-U12323-1Q.Seq.d
          Length = 1373

 Score = 36.2 bits (18), Expect = 0.035
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                              
Query: 211  gaataaaaataataaata 228
            ||||||||||||||||||
Sbjct: 1337 gaataaaaataataaata 1354


 Score = 28.2 bits (14), Expect = 8.4
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                          
Query: 257  ttcttaataaattt 270
            ||||||||||||||
Sbjct: 1309 ttcttaataaattt 1322


  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: 10,817
Number of Sequences: 6905
Number of extensions: 10817
Number of successful extensions: 1524
Number of sequences better than 10.0: 607
length of query: 498
length of database: 5,674,871
effective HSP length: 16
effective length of query: 482
effective length of database: 5,564,391
effective search space: 2682036462
effective search space used: 2682036462
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. 5.12
Homology vs DNA 
Query= Contig-U02018-1 (Contig-U02018-1Q) /CSM_Contig/Contig-U02018-1Q.Seq.d
         (498 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

(C93158) Dictyostelium discoideum slug cDNA, clone SSM694.        226   6e-66  2
(FH571373) CHO_OF4297xd10r1.ab1 CHO_OF4 Nicotiana tabacum ge...    36   0.064  2
(FH643486) CHO_OF4977xi18r1.ab1 CHO_OF4 Nicotiana tabacum ge...    36   0.064  2
(FH726301) CHO_OF5088xg04r1.ab1 CHO_OF5 Nicotiana tabacum ge...    36   0.064  2
(AC137389) Rattus norvegicus clone CH230-unknown, *** SEQUEN...    46   1.3    1
(AC137388) Rattus norvegicus clone CH230-unknown, *** SEQUEN...    46   1.3    1
(AC129651) Rattus norvegicus clone CH230-9A14, *** SEQUENCIN...    46   1.3    1
(AC098215) Rattus norvegicus clone CH230-111K1, *** SEQUENCI...    46   1.3    1
(AP009095) Marchantia polymorpha genomic DNA, chromosome Y, ...    46   1.3    1
(AC198286) Spermophilus tridecemlineatus clone VMRC20-645I11...    46   1.3    1
(AC164340) Bos taurus clone CH240-150O10, *** SEQUENCING IN ...    46   1.3    1
(Z82561) R.prowazekii genomic DNA fragment (clone A23F).           46   1.3    1
(AJ235271) Rickettsia prowazekii strain Madrid E, complete g...    46   1.3    1
(AM433314) Vitis vinifera contig VV78X034330.5, whole genome...    42   2.4    2
(AC156287) Mus musculus 6 BAC RP24-243F8 (Roswell Park Cance...    44   5.0    1
(AC153616) Mus musculus 6 BAC RP23-328I7 (Roswell Park Cance...    44   5.0    1
(AM487261) Vitis vinifera contig VV78X198279.13, whole genom...    44   5.0    1
(AC234224) Felis catus BAC clone FCAB-64H12 from chromosome ...    44   5.0    1
(AC159479) Mus musculus clone RP24-81H11, WORKING DRAFT SEQU...    44   5.0    1
(EK422881) 1095515638656 Global-Ocean-Sampling_GS-31-01-01-1...    44   5.0    1
(DW539183) EST_ssal_rgb2_3602 rgb2 Salmo salar cDNA clone ss...    44   5.0    1
(FG612312) stem_S083_D08.SEQ Opium poppy stem cDNA library P...    44   5.0    1
(FG608321) stem_S033_G09.SEQ Opium poppy stem cDNA library P...    44   5.0    1
(CT573471) Zebrafish DNA sequence from clone DKEY-30J10 in l...    30   9.4    2

>(C93158) Dictyostelium discoideum slug cDNA, clone SSM694.
          Length = 499

 Score =  226 bits (114), Expect(2) = 6e-66
 Identities = 114/114 (100%)
 Strand = Plus / Plus


Query: 98  caagtattaccaggttgggaaattagaagatttgaagataagaaaaagaaattcattttt 157
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 98  caagtattaccaggttgggaaattagaagatttgaagataagaaaaagaaattcattttt 157


Query: 158 gtagcgcctaatggtgacgaaaaatgttattatcttaaacatgcattacaatgg 211
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 158 gtagcgcctaatggtgacgaaaaatgttattatcttaaacatgcattacaatgg 211

 Score = 61.9 bits (31), Expect(2) = 6e-66
 Identities = 31/31 (100%)
 Strand = Plus / Plus


Query: 405 catctttaattactagtagtaatactagtag 435
           |||||||||||||||||||||||||||||||
Sbjct: 405 catctttaattactagtagtaatactagtag 435

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 193,416,954
Number of extensions: 13399641
Number of successful extensions: 1217280
Number of sequences better than 10.0: 24
Length of query: 498
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 475
Effective length of database: 99,442,330,388
Effective search space: 47235106934300
Effective search space used: 47235106934300
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U02018-1 (Contig-U02018-1Q) /CSM_Contig/Contig-U02018-1Q.Seq.d
         (498 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AB255366_3(AB255366|pid:none) Staphylococcus aureus IMCJ1379 pla...    38   0.15
CP000123_428(CP000123|pid:none) Mycoplasma capricolum subsp. cap...    35   0.96
AP008981_1525(AP008981|pid:none) Orientia tsutsugamushi str. Ike...    34   1.6
AL929357_69(AL929357|pid:none) Plasmodium falciparum strain 3D7,...    34   1.6
AL844508_227(AL844508|pid:none) Plasmodium falciparum 3D7 chromo...    34   1.6
T23731(T23731)hypothetical protein M05D6.2 - Caenorhabditis eleg...    34   2.1
CP000246_372(CP000246|pid:none) Clostridium perfringens ATCC 131...    34   2.1
Z50044_10(Z50044|pid:none) Caenorhabditis elegans Cosmid F22B5, ...    34   2.1
AE014187_343(AE014187|pid:none) Plasmodium falciparum 3D7 chromo...    33   2.9
AL844502_77(AL844502|pid:none) Plasmodium falciparum 3D7 chromos...    33   3.7
AX647673_1(AX647673|pid:none) Sequence 1865 from Patent EP1270724.     33   4.9
CP000236_452(CP000236|pid:none) Ehrlichia chaffeensis str. Arkan...    32   6.3
CP000517_468(CP000517|pid:none) Lactobacillus helveticus DPC 457...    32   6.3
BC167592_1(BC167592|pid:none) Xenopus tropicalis hypothetical pr...    32   8.2
AE014188_223(AE014188|pid:none) Plasmodium falciparum 3D7 chromo...    32   8.2
AC132211_1(AC132211|pid:none) Caenorhabditis elegans cosmid Y108...    32   8.2

>AB255366_3(AB255366|pid:none) Staphylococcus aureus IMCJ1379
           plasmid pSA1379 DNA, complete sequence.
           &AB304512_42(AB304512|pid:none)
           &AP003139_3(AP003139|pid:none)
           &CP000704_19(CP000704|pid:none)
           &CP000731_3(CP000731|pid:none)
           &CP000737_5(CP000737|pid:none)
          Length = 230

 Score = 37.7 bits (86), Expect = 0.15
 Identities = 32/103 (31%), Positives = 52/103 (50%), Gaps = 9/103 (8%)
 Frame = +2

Query: 26  KEILEREKLKFKN-----FKTNYKIERFRQVLPGWEIRRFEDKKKKFIFVAPNGDEKCYY 190
           KEI   E+L+ KN     F+   K E F+++       + EDK  K  ++A   ++K
Sbjct: 55  KEISFLEQLQNKNEDMQKFEKQMKKEGFKKI-------KLEDKNSKLKYLATEANDK--- 104

Query: 191 LKHALQWNKNNKY-GEKIKDV---ESFLINFNKDVKKQISDKR 307
             +A  +  NN Y  EK K++   E+   N+NK + K I++KR
Sbjct: 105 --NAYGYIANNAYKNEKTKEIVVSETIYDNYNKKITKFIAEKR 145

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: 420,750,532
Number of extensions: 7599827
Number of successful extensions: 31336
Number of sequences better than 10.0: 16
Number of HSP's gapped: 31317
Number of HSP's successfully gapped: 16
Length of query: 166
Length of database: 1,051,180,864
Length adjustment: 119
Effective length of query: 47
Effective length of database: 666,030,343
Effective search space: 31303426121
Effective search space used: 31303426121
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: 30 (16.2 bits)
PSORT 

 psg: 0.36  gvh: 0.11  alm: 0.64  top: 0.53  tms: 0.00  mit: 0.17  mip: 0.00
 nuc: 0.37  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 

	 72.0 %: nuclear
	 16.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: cytoskeletal

>> prediction for Contig-U02018-1 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