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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-U13130-1
Contig ID Contig-U13130-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13130-1 (Contig-U13130-1Q) /CSM_Contig/Contig-U13130-1Q.Seq.d
NNNNNNNNNNAACATTNTCAGCNCAATCAACATAATCAGCATAATCNACA
TAATCAGCCCAATCNACATAATCNACATAATCNAGCATAATCNACATAAT
CNACATAATCAACATAATCNACATAATCNACATAATCNACTTAATCAACA
TAATCCNCTTAACCCACATAATCCACATAACCTACTTAATCCACTTAATC
GACATAATCCNCTTGACCCACATAATCCACATAATCCACATTTTCACCAC
CATCACCATCACCATCATCACCNCCATCCTCCTATGGTCCCAAGNTTTTT
TTATCAACAACCACCACAACAACCAACAGCAGCACCNCCACCTTTACAAC
AAAGAAGATATATTAATCAAGGTAATTNTTTAAATGATCCAATAACATTA
GANTTTGGTGATGTTTCAACCGATTAGAAATAATACCAAATCAAAATAAA
TAAAAATATAAAAAATAACTTTAAAAAAATAAAATAAAAAAAAAATGAAA
ACACATTCAATGAAAATGTAAGGAGGAGCACACAAAAAATAAAAAAATAA
AAACATCACAACAGTAAAAAATGAAAATGTAAGAGTATTCTAAAAAAAAT
AAAAAAAAT
Gap no gap
Contig length 609
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 26648
End point 26929
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U13130
List of clone(s) 

est1=CHQ250Z,1,600
Translated Amino Acid sequence 
XXXNIXSXINIISIIXIISPIXIIXIIXHNXHNXHNQHNXHNXHNXLNQHNPLNPHNPHN
LLNPLNRHNPLDPHNPHNPHFHHHHHHHHHXHPPMVPXFFYQQPPQQPTAAPPPLQQRRY
INQGNXLNDPITLXFGDVSTD*k*yqikinkniknnfkkik*kknentfnenvrrstqki
kk*khhnskk*kcksilkkikk
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxhxqxnqhnqhnxhnqpnxhnxhnxa*st*st*st*st*st*st*st*sx*pt*st*
pt*st*st*sx*pt*st*stfsppspspssppssygpkxflsttttttnsstxtfttkki
y*sr*xfk*snnirxw*cfnrleiipnqnk*kykk*l*knkikkk*khiq*kckeehtkn
kkiktsqq*kmkm*eyskknkkn


Frame B:
XXXNIXSXINIISIIXIISPIXIIXIIXHNXHNXHNQHNXHNXHNXLNQHNPLNPHNPHN
LLNPLNRHNPLDPHNPHNPHFHHHHHHHHHXHPPMVPXFFYQQPPQQPTAAPPPLQQRRY
INQGNXLNDPITLXFGDVSTD*k*yqikinkniknnfkkik*kknentfnenvrrstqki
kk*khhnskk*kcksilkkikk


Frame C:
xxxtxsaqst*sa*st*saqst*st*ssiixiixiiniixiixiixliniixlthiihit
ylihlidiixlthiihiihifttititiitxillwsqxffinnhhnnqqqhxhlynkedi
likvix*miq*h*xlvmfqpirnntksk*iki*kitlkk*nkkkmkthsmkm*ggahkk*
knknittvknenvrvf*kk*kk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13130-1 (Contig-U13130-1Q)
/CSM_Contig/Contig-U13130-1Q.Seq.d
         (609 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13130-1 (Contig-U13130-1Q) /CSM_Contig/Conti...   262  4e-70
Contig-U10935-1 (Contig-U10935-1Q) /CSM_Contig/Conti...    46  4e-05
Contig-U14360-1 (Contig-U14360-1Q) /CSM_Contig/Conti...    42  7e-04
Contig-U13852-1 (Contig-U13852-1Q) /CSM_Contig/Conti...    42  7e-04
Contig-U14170-1 (Contig-U14170-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U05561-1 (Contig-U05561-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U14547-1 (Contig-U14547-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U14518-1 (Contig-U14518-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U13909-1 (Contig-U13909-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U12710-1 (Contig-U12710-1Q) /CSM_Contig/Conti...    38  0.011

>Contig-U13130-1 (Contig-U13130-1Q) /CSM_Contig/Contig-U13130-1Q.Seq.d
          Length = 609

 Score =  262 bits (132), Expect = 4e-70
 Identities = 158/165 (95%)
 Strand = Plus / Plus

                                                                       
Query: 278 cctcctatggtcccaagnnnnnnnnatcaacaaccaccacaacaaccaacagcagcaccn 337
           ||||||||||||||||||       |||||||||||||||||||||||||||||||||||
Sbjct: 278 cctcctatggtcccaagntttttttatcaacaaccaccacaacaaccaacagcagcaccn 337

                                                                       
Query: 338 ccacctttacaacaaagaagatatattaatcaaggtaattntttaaatgatccaataaca 397
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 338 ccacctttacaacaaagaagatatattaatcaaggtaattntttaaatgatccaataaca 397

                                                        
Query: 398 ttagantttggtgatgtttcaaccgattagaaataataccaaatc 442
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 398 ttagantttggtgatgtttcaaccgattagaaataataccaaatc 442


 Score =  170 bits (86), Expect = 1e-42
 Identities = 95/95 (100%)
 Strand = Plus / Plus

                                                                       
Query: 130 acataatcnacttaatcaacataatccncttaacccacataatccacataacctacttaa 189
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 130 acataatcnacttaatcaacataatccncttaacccacataatccacataacctacttaa 189

                                              
Query: 190 tccacttaatcgacataatccncttgacccacata 224
           |||||||||||||||||||||||||||||||||||
Sbjct: 190 tccacttaatcgacataatccncttgacccacata 224


 Score = 89.7 bits (45), Expect = 3e-18
 Identities = 54/54 (100%)
 Strand = Plus / Plus

                                                                
Query: 11 aacattntcagcncaatcaacataatcagcataatcnacataatcagcccaatc 64
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11 aacattntcagcncaatcaacataatcagcataatcnacataatcagcccaatc 64


 Score = 75.8 bits (38), Expect = 5e-14
 Identities = 38/38 (100%)
 Strand = Plus / Plus

                                                 
Query: 496 tgaaaacacattcaatgaaaatgtaaggaggagcacac 533
           ||||||||||||||||||||||||||||||||||||||
Sbjct: 496 tgaaaacacattcaatgaaaatgtaaggaggagcacac 533


 Score = 75.8 bits (38), Expect = 5e-14
 Identities = 38/38 (100%)
 Strand = Plus / Plus

                                                 
Query: 554 catcacaacagtaaaaaatgaaaatgtaagagtattct 591
           ||||||||||||||||||||||||||||||||||||||
Sbjct: 554 catcacaacagtaaaaaatgaaaatgtaagagtattct 591


 Score = 67.9 bits (34), Expect = 1e-11
 Identities = 45/48 (93%)
 Strand = Plus / Plus

                                                           
Query: 133 taatcnacttaatcaacataatccncttaacccacataatccacataa 180
           ||||| |||||||| ||||||||||||| |||||||||||||||||||
Sbjct: 187 taatccacttaatcgacataatccncttgacccacataatccacataa 234


 Score = 67.9 bits (34), Expect = 1e-11
 Identities = 70/83 (84%)
 Strand = Plus / Plus

                                                                       
Query: 142 taatcaacataatccncttaacccacataatccacataacctacttaatccacttaatcg 201
           ||||| ||||||||  | ||| | |||||||| |||||| | || ||||| |||||||| 
Sbjct: 88  taatcnacataatcnacataatcaacataatcnacataatcnacataatcnacttaatca 147

                                  
Query: 202 acataatccncttgacccacata 224
           ||||||||||||| |||||||||
Sbjct: 148 acataatccncttaacccacata 170


 Score = 54.0 bits (27), Expect = 2e-07
 Identities = 67/81 (82%)
 Strand = Plus / Plus

                                                                       
Query: 130 acataatcnacttaatcaacataatccncttaacccacataatccacataacctacttaa 189
           ||||||||||| ||||||||||||||  | ||| | |||||||| || ||| | || |||
Sbjct: 94  acataatcnacataatcaacataatcnacataatcnacataatcnacttaatcaacataa 153

                                
Query: 190 tccacttaatcgacataatcc 210
           ||| ||||| | |||||||||
Sbjct: 154 tccncttaacccacataatcc 174


 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 29/31 (93%)
 Strand = Plus / Plus

                                          
Query: 25  aatcaacataatcagcataatcnacataatc 55
           |||||||||||||  ||||||||||||||||
Sbjct: 107 aatcaacataatcnacataatcnacataatc 137


 Score = 36.2 bits (18), Expect = 0.043
 Identities = 27/31 (87%)
 Strand = Plus / Plus

                                          
Query: 25  aatcaacataatcagcataatcnacataatc 55
           |||| ||||||||  ||||||| ||||||||
Sbjct: 89  aatcnacataatcnacataatcaacataatc 119


 Score = 36.2 bits (18), Expect = 0.043
 Identities = 36/43 (83%)
 Strand = Plus / Plus

                                                      
Query: 167 cataatccacataacctacttaatccacttaatcgacataatc 209
           ||||||| |||||| | || ||||| || ||||| ||||||||
Sbjct: 86  cataatcnacataatcnacataatcaacataatcnacataatc 128


 Score = 34.2 bits (17), Expect = 0.17
 Identities = 28/31 (90%)
 Strand = Plus / Plus

                                         
Query: 25 aatcaacataatcagcataatcnacataatc 55
          |||| |||||||||||  |||||||||||||
Sbjct: 43 aatcnacataatcagcccaatcnacataatc 73


 Score = 32.2 bits (16), Expect = 0.66
 Identities = 25/29 (86%)
 Strand = Plus / Plus

                                       
Query: 18 tcagcncaatcaacataatcagcataatc 46
          ||||| ||||| ||||||||  |||||||
Sbjct: 54 tcagcccaatcnacataatcnacataatc 82


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 164 ccacataatccacat 178
           |||||||||||||||
Sbjct: 227 ccacataatccacat 241


>Contig-U10935-1 (Contig-U10935-1Q) /CSM_Contig/Contig-U10935-1Q.Seq.d
          Length = 2315

 Score = 46.1 bits (23), Expect = 4e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                  
Query: 303 atcaacaaccaccacaacaacca 325
           |||||||||||||||||||||||
Sbjct: 141 atcaacaaccaccacaacaacca 163


 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 305 caacaaccaccacaacaacca 325
           |||||||||||||||||||||
Sbjct: 221 caacaaccaccacaacaacca 241


 Score = 36.2 bits (18), Expect = 0.043
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                 
Query: 305 caacaaccaccacaacaaccaa 326
           |||||||||| |||||||||||
Sbjct: 428 caacaaccacaacaacaaccaa 449


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 18/19 (94%)
 Strand = Plus / Plus

                              
Query: 307 acaaccaccacaacaacca 325
           ||||| |||||||||||||
Sbjct: 106 acaacaaccacaacaacca 124


>Contig-U14360-1 (Contig-U14360-1Q) /CSM_Contig/Contig-U14360-1Q.Seq.d
          Length = 297

 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 303 atcaacaaccaccacaacaac 323
           |||||||||||||||||||||
Sbjct: 211 atcaacaaccaccacaacaac 231


  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: 3830
Number of Sequences: 6905
Number of extensions: 3830
Number of successful extensions: 743
Number of sequences better than 10.0: 166
length of query: 609
length of database: 5,674,871
effective HSP length: 16
effective length of query: 593
effective length of database: 5,564,391
effective search space: 3299683863
effective search space used: 3299683863
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2008.12. 6
Homology vs DNA 
Query= Contig-U13130-1 (Contig-U13130-1Q) /CSM_Contig/Contig-U13130-1Q.Seq.d
         (609 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

(BJ385306) Dictyostelium discoideum cDNA clone:ddc54c14, 3' ...   230   3e-91  4
(AC097951) Rattus norvegicus clone CH230-127O19, *** SEQUENC...    36   0.057  2
(AC132707) Rattus norvegicus clone CH230-288M15, WORKING DRA...    36   0.057  2
(AC119114) Rattus norvegicus clone CH230-245F12, WORKING DRA...    36   0.058  2
(AC139614) Rattus norvegicus clone CH230-105D22, *** SEQUENC...    48   0.37   1
(CU432286) Clytia hemisphaerica 5-PRIME EST from clone SA0AA...    42   0.82   2
(CU463045) Medicago truncatula chromosome 5 clone mth4-4e12,...    46   1.5    1
(AC115612) Dictyostelium discoideum chromosome 2 map 6245135...    46   1.5    1
(CU475569) Medicago truncatula chromosome 5 clone mte1-16h18...    46   1.5    1
(CR299049) mte1-16H18FM1 BAC end, cultivar Jemalong A17 of M...    46   1.5    1
(AG491310) Mus musculus molossinus DNA, clone:MSMg01-388O22....    46   1.5    1
(BM415123) OP20195 Mixed Stage EST's from Globodera pallida,...    46   1.5    1
(BJ392337) Dictyostelium discoideum cDNA clone:dds27d12, 5' ...    46   1.5    1
(EY474809) META948TF JCVI-MT3 Medicago truncatula cDNA 5', m...    46   1.5    1
(AC111108) Mus musculus chromosome 8 clone RP23-197P15 map 8...    32   2.8    2
(AC121116) Mus musculus chromosome 8, clone RP23-267D22, com...    32   2.8    2
(AC154507) Mus musculus BAC clone RP24-95E21 from chromosome...    44   5.8    1
(AY040537) Locusta migratoria hunchback transcription factor...    44   5.8    1
(AE014296) Drosophila melanogaster chromosome 3L, complete s...    44   5.8    1
(AC091219) Drosophila melanogaster 3L BAC RP98-4C3 (Roswell ...    44   5.8    1
(AC010057) Drosophila melanogaster 3L BAC RP98-26C18 (Roswel...    44   5.8    1
(AC126063) Rattus norvegicus clone CH230-11C10, *** SEQUENCI...    44   5.8    1
(CT956026) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.8    1
(AC019753) Drosophila melanogaster, *** SEQUENCING IN PROGRE...    44   5.8    1
(CT192090) Sus scrofa genomic clone PigE-94E1, genomic surve...    44   5.8    1

>(BJ385306) Dictyostelium discoideum cDNA clone:ddc54c14, 3' end,
           single read.
          Length = 600

 Score =  230 bits (116), Expect(4) = 3e-91
 Identities = 125/125 (100%)
 Strand = Plus / Minus


Query: 303 atcaacaaccaccacaacaaccaacagcagcaccnccacctttacaacaaagaagatata 362
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 308 atcaacaaccaccacaacaaccaacagcagcaccnccacctttacaacaaagaagatata 249


Query: 363 ttaatcaaggtaattntttaaatgatccaataacattagantttggtgatgtttcaaccg 422
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 248 ttaatcaaggtaattntttaaatgatccaataacattagantttggtgatgtttcaaccg 189


Query: 423 attag 427
           |||||
Sbjct: 188 attag 184

 Score =  109 bits (55), Expect(4) = 3e-91
 Identities = 58/58 (100%)
 Strand = Plus / Minus


Query: 158 cttaacccacataatccacataacctacttaatccacttaatcgacataatccncttg 215
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 453 cttaacccacataatccacataacctacttaatccacttaatcgacataatccncttg 396

 Score = 46.1 bits (23), Expect(4) = 3e-91
 Identities = 29/29 (100%)
 Strand = Plus / Minus


Query: 11  aacattntcagcncaatcaacataatcag 39
           |||||||||||||||||||||||||||||
Sbjct: 600 aacattntcagcncaatcaacataatcag 572

 Score = 32.2 bits (16), Expect(4) = 3e-91
 Identities = 16/16 (100%)
 Strand = Plus / Minus


Query: 279 ctcctatggtcccaag 294
           ||||||||||||||||
Sbjct: 332 ctcctatggtcccaag 317

 Score = 38.2 bits (19), Expect(2) = 8.0
 Identities = 37/44 (84%)
 Strand = Plus / Minus


Query: 166 acataatccacataacctacttaatccacttaatcgacataatc 209
           |||||||| |||||| | || ||||| || ||||| ||||||||
Sbjct: 517 acataatcnacataatcaacataatcnacataatcnacataatc 474

 Score = 28.2 bits (14), Expect(2) = 8.0
 Identities = 18/20 (90%)
 Strand = Plus / Minus


Query: 18  tcagcncaatcaacataatc 37
           ||||| ||||| ||||||||
Sbjct: 557 tcagcccaatcnacataatc 538

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 167,026,764
Number of extensions: 9802856
Number of successful extensions: 727152
Number of sequences better than 10.0: 25
Length of query: 609
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 586
Effective length of database: 93,106,754,628
Effective search space: 54560558212008
Effective search space used: 54560558212008
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13130-1 (Contig-U13130-1Q) /CSM_Contig/Contig-U13130-1Q.Seq.d
         (609 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: 227,452,916
Number of extensions: 1535614
Number of successful extensions: 3566
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3436
Number of HSP's successfully gapped: 0
Length of query: 203
Length of database: 1,051,180,864
Length adjustment: 122
Effective length of query: 81
Effective length of database: 656,320,666
Effective search space: 53161973946
Effective search space used: 53161973946
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: 0.46  alm: 0.19  top: 0.63  tms: 0.07  mit: 0.32  mip: 0.19
 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: 1.00  tyr: 0.00  leu: 0.04  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 1.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 44.0 %: nuclear
	 28.0 %: cytoplasmic
	 12.0 %: mitochondrial
	  8.0 %: Golgi
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U13130-1 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) 0
CH (FL, L) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0