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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-U04879-1
Contig ID Contig-U04879-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04879-1 (Contig-U04879-1Q) /CSM_Contig/Contig-U04879-1Q.Seq.d
CCTTTATATAAATAAAAAAAATAAAAAAAAACAATAAAATATAAAATAAT
AATAATAAAAAAACAAAAAAATAAAGAAAAAAATCAAAAAATCAAAGAAT
AAAAATGTTAGATAAAATATTTTCTTTTAAATTCTCAAATTCAATTAGAG
AGAGTGTAAATCGTTTAGTTTTAAACCATGAAAGACGTCATATTGAATAC
GAGAAAATGAGGGAAATTCACAAGAGATATTGGCAACAACATTTCCACAA
TTATGAATACTCTCATCACTATGGCCATCGTCGAACTAATTGTGGTTGTA
ATGGAAATAGAAATACCAACAATACCTCCTCTAATAATAATAATACCAAC
AACTACAACAATACCACTTCCAACAATAGTAACAGTAACACCAATAACAA
CAACACAAATAATAATAATAATACTGGTGGTTTTAGATTTAGAGATTATT
GGTTTTCTCAGCATAACAATTTCCATAATAAAAGTCACAGTTATTTTAGA
TCACATTTCTATAATCATTCAAATCGTAGATATTATAATAGAGCAAACAA
GTGTAATGATAA
Gap no gap
Contig length 562
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 2616612
End point 2616050
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U04879
List of clone(s) 

est1=SSD575F,1,563
Translated Amino Acid sequence 
fi*ikkikknnki*nnnnkktkk*RKKSKNQRIKMLDKIFSFKFSNSIRESVNRLVLNHE
RRHIEYEKMREIHKRYWQQHFHNYEYSHHYGHRRTNCGCNGNRNTNNTSSNNNNTNNYNN
TTSNNSNSNTNNNNTNNNNNTGGFRFRDYWFSQHNNFHNKSHSYFRSHFYNHSNRRYYNR
ANKCND
Translated Amino Acid sequence (All Frames) 
Frame A:
plyk*kk*kktikykiiiikkqknkeknqkike*kc*ikyfllnsqiqlerv*iv*f*tm
kdvilntrk*gkftrdignnistimntlitmaivelivvvmeieiptippliiiiptttt
iplptivtvtpitttqiiiiilvvldleiigflsitisiikvtvildhisiiiqivdiii
eqtsvmi


Frame B:
lyinkknkkkq*nik****knkkikkkikksknknvr*niff*ilkfn*recksfsfkp*
ktsy*irenegnsqeilattfpql*ilsslwpssn*lwl*wk*kyqqyll****yqqlqq
yhfqq**q*hq*qqhk****ywwf*i*rllvfsa*qfp**ksqlf*itfl*sfks*il**
skqv***


Frame C:
fi*ikkikknnki*nnnnkktkk*RKKSKNQRIKMLDKIFSFKFSNSIRESVNRLVLNHE
RRHIEYEKMREIHKRYWQQHFHNYEYSHHYGHRRTNCGCNGNRNTNNTSSNNNNTNNYNN
TTSNNSNSNTNNNNTNNNNNTGGFRFRDYWFSQHNNFHNKSHSYFRSHFYNHSNRRYYNR
ANKCND
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04879-1 (Contig-U04879-1Q)
/CSM_Contig/Contig-U04879-1Q.Seq.d
         (562 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04879-1 (Contig-U04879-1Q) /CSM_Contig/Conti...   490  e-139
Contig-U07040-1 (Contig-U07040-1Q) /CSM_Contig/Conti...    42  6e-04
Contig-U11379-1 (Contig-U11379-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U08981-1 (Contig-U08981-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U11807-1 (Contig-U11807-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U12492-1 (Contig-U12492-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U11431-1 (Contig-U11431-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U11299-1 (Contig-U11299-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U11018-1 (Contig-U11018-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U08262-1 (Contig-U08262-1Q) /CSM_Contig/Conti...    36  0.039

>Contig-U04879-1 (Contig-U04879-1Q) /CSM_Contig/Contig-U04879-1Q.Seq.d
          Length = 562

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

                                                                       
Query: 106 tgttagataaaatattttcttttaaattctcaaattcaattagagagagtgtaaatcgtt 165
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106 tgttagataaaatattttcttttaaattctcaaattcaattagagagagtgtaaatcgtt 165

                                                                       
Query: 166 tagttttaaaccatgaaagacgtcatattgaatacgagaaaatgagggaaattcacaaga 225
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 166 tagttttaaaccatgaaagacgtcatattgaatacgagaaaatgagggaaattcacaaga 225

                                                                       
Query: 226 gatattggcaacaacatttccacaattatgaatactctcatcactatggccatcgtcgaa 285
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 226 gatattggcaacaacatttccacaattatgaatactctcatcactatggccatcgtcgaa 285

                                                                       
Query: 286 ctaattgtggttgtaatggaaatagaaataccaacaatacctcctctaataataataata 345
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 286 ctaattgtggttgtaatggaaatagaaataccaacaatacctcctctaataataataata 345

                  
Query: 346 ccaacaa 352
           |||||||
Sbjct: 346 ccaacaa 352


 Score =  289 bits (146), Expect = 2e-78
 Identities = 146/146 (100%)
 Strand = Plus / Plus

                                                                       
Query: 417 aataatactggtggttttagatttagagattattggttttctcagcataacaatttccat 476
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 417 aataatactggtggttttagatttagagattattggttttctcagcataacaatttccat 476

                                                                       
Query: 477 aataaaagtcacagttattttagatcacatttctataatcattcaaatcgtagatattat 536
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 477 aataaaagtcacagttattttagatcacatttctataatcattcaaatcgtagatattat 536

                                     
Query: 537 aatagagcaaacaagtgtaatgataa 562
           ||||||||||||||||||||||||||
Sbjct: 537 aatagagcaaacaagtgtaatgataa 562


 Score = 30.2 bits (15), Expect = 2.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 332 taataataataatac 346
           |||||||||||||||
Sbjct: 410 taataataataatac 424


>Contig-U07040-1 (Contig-U07040-1Q) /CSM_Contig/Contig-U07040-1Q.Seq.d
          Length = 521

 Score = 42.1 bits (21), Expect = 6e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 332 taataataataataccaacaa 352
           |||||||||||||||||||||
Sbjct: 397 taataataataataccaacaa 417


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 457 taataataataata 470


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 391 taataataataata 404


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 394 taataataataata 407


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 460 taataataataata 473


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 436 taataataataata 449


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 388 taataataataata 401


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 433 taataataataata 446


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 439 taataataataata 452


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 442 taataataataata 455


>Contig-U11379-1 (Contig-U11379-1Q) /CSM_Contig/Contig-U11379-1Q.Seq.d
          Length = 1752

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 332 taataataataataccaaca 351
           ||||||||||||||||||||
Sbjct: 330 taataataataataccaaca 349


 Score = 30.2 bits (15), Expect = 2.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 331 ctaataataataata 345
           |||||||||||||||
Sbjct: 311 ctaataataataata 325


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 321 taataataataata 334


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 315 taataataataata 328


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 324 taataataataata 337


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 327 taataataataata 340


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 331 ctaataataataat 344
           ||||||||||||||
Sbjct: 392 ctaataataataat 405


 Score = 28.2 bits (14), Expect = 9.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 332 taataataataata 345
           ||||||||||||||
Sbjct: 318 taataataataata 331


  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: 19,168
Number of Sequences: 6905
Number of extensions: 19168
Number of successful extensions: 9248
Number of sequences better than 10.0: 1608
length of query: 562
length of database: 5,674,871
effective HSP length: 16
effective length of query: 546
effective length of database: 5,564,391
effective search space: 3038157486
effective search space used: 3038157486
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. 7. 5
Homology vs DNA 
Query= Contig-U04879-1 (Contig-U04879-1Q) /CSM_Contig/Contig-U04879-1Q.Seq.d
         (562 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

(AU072169) Dictyostelium discoideum slug cDNA, clone SSD575.      186   6e-43  1
(AC162118) Chlorocebus aethiops clone CH252-338D10, WORKING ...    46   1.4    1
(AC206607) Zea mays chromosome 1 clone CH201-320H13; ZMMBBc0...    46   1.4    1
(AG614149) Macaca fuscata fuscata DNA, clone: MSB2-002I14_F,...    34   3.8    2
(CR376864) Pan troglodytes chromosome X BAC PTB-045G22.            44   5.7    1
(AC108368) Pan troglodytes clone S10883.BCM-13, WORKING DRAF...    44   5.7    1
(AC108367) Pan troglodytes clone S10883.BCM-12, WORKING DRAF...    44   5.7    1
(AC108366) Pan troglodytes clone S10883.BCM-11, WORKING DRAF...    44   5.7    1
(AC107036) Pan troglodytes clone S10883.BCM-9, *** SEQUENCIN...    44   5.7    1
(CU928840) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.7    1
(AC221229) Bos taurus clone CH240-400E24, WORKING DRAFT SEQU...    44   5.7    1
(EI685428) SB_BBd05-O15.F SB_BBd Sorghum bicolor genomic 5',...    44   5.7    1
(CU165243) Equus caballus GSS, BAC clone CH241-288L13, SP6 e...    44   5.7    1
(DN198012) USDA-FP_134726 5th Instar Glassy-winged Sharpshoo...    44   5.7    1
(EY487075) CBBP15582.rev CBBP Hirudo medicinalis hermaphrodi...    44   5.7    1
(AE017245) Mycoplasma synoviae 53, complete genome.                44   5.7    1

>(AU072169) Dictyostelium discoideum slug cDNA, clone SSD575.
          Length = 240

 Score =  186 bits (94), Expect = 6e-43
 Identities = 94/94 (100%)
 Strand = Plus / Plus


Query: 147 agagagagtgtaaatcgtttagttttaaaccatgaaagacgtcatattgaatacgagaaa 206
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 147 agagagagtgtaaatcgtttagttttaaaccatgaaagacgtcatattgaatacgagaaa 206


Query: 207 atgagggaaattcacaagagatattggcaacaac 240
           ||||||||||||||||||||||||||||||||||
Sbjct: 207 atgagggaaattcacaagagatattggcaacaac 240

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 386,155,953
Number of extensions: 21260994
Number of successful extensions: 1534026
Number of sequences better than 10.0: 16
Length of query: 562
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 539
Effective length of database: 99,442,330,388
Effective search space: 53599416079132
Effective search space used: 53599416079132
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.31
Homology vs Protein 
Query= Contig-U04879-1 (Contig-U04879-1Q) /CSM_Contig/Contig-U04879-1Q.Seq.d
         (562 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AL034557_45(AL034557|pid:none) Plasmodium falciparum MAL4P1.  &A...    36   0.80
AP008218_871(AP008218|pid:none) Oryza sativa (japonica cultivar-...    35   1.0
AE014298_1091(AE014298|pid:none) Drosophila melanogaster chromos...    35   1.4
AL844508_102(AL844508|pid:none) Plasmodium falciparum 3D7 chromo...    33   4.0
CP000319_3414(CP000319|pid:none) Nitrobacter hamburgensis X14, c...    33   5.2
AL844509_46(AL844509|pid:none) Plasmodium falciparum 3D7 chromos...    33   5.2
(Q1ZXH2) RecName: Full=Probable serine/threonine-protein kinase ...    33   6.8

>AL034557_45(AL034557|pid:none) Plasmodium falciparum MAL4P1.
            &AL844503_44(AL844503|pid:none)
          Length = 4138

 Score = 35.8 bits (81), Expect = 0.80
 Identities = 11/33 (33%), Positives = 21/33 (63%)
 Frame = +3

Query: 462  HNNFHNKSHSYFRSHFYNHSNRRYYNRANKCND 560
            HNN+HN  H+ + ++++N+ N  Y N  +  N+
Sbjct: 919  HNNYHNNYHNNYHNNYHNNQNNNYNNLCSSWNE 951

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: 421,899,459
Number of extensions: 5963271
Number of successful extensions: 29983
Number of sequences better than 10.0: 7
Number of HSP's gapped: 29091
Number of HSP's successfully gapped: 9
Length of query: 187
Length of database: 1,061,185,681
Length adjustment: 121
Effective length of query: 66
Effective length of database: 665,703,473
Effective search space: 43936429218
Effective search space used: 43936429218
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: 0.75  gvh: 0.35  alm: 0.58  top: 0.53  tms: 0.00  mit: 0.37  mip: 0.03
 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
	 24.0 %: mitochondrial
	 20.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  4.0 %: extracellular, including cell wall
	  4.0 %: peroxisomal

>> prediction for Contig-U04879-1 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