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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U09800-1
Contig ID Contig-U09800-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U09800-1 (Contig-U09800-1Q) /CSM_Contig/Contig-U09800-1Q.Seq.d
GNACACTCTAATAGTAGTTAATTGTGTAATATTAAATAAATATTATTATT
TTGTACCATTACTTTATAAACAAAAAAAAAAAACCAAAAAAAAAACCAAA
AAAAAA----------ANNNAAAAAAAAANTTTTTTTTNNGNCCCCCNTT
TTTTTTCCCNAAAAAAAAAACCCNAAAAAAANCCCNAAAAAAAAAAAAAA
AAAAAAAAATTTTTTTTTTTTTTANCCCCNTTNNAAAACCNNCCNTTTTT
TCCNNNAAAAAAAAAAAAAAAAAAAAAATTA
Gap gap included
Contig length 271
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 2
Link to clone list U09800
List of clone(s) 

est1=VSG302F,1,107
est2=VSG302Z,108,273
Translated Amino Acid sequence 
XTLIVVNCVILNKYYYFVPLLYKQKKKTKKKTKKK---

---XXKKXFFXXPXFFSXKKKPXKXPXKKKKKKKFFFFLXPXXNXPFFPXKKKKKKKL
Translated Amino Acid sequence (All Frames) 
Frame A:
xhsnss*lcnik*illfctitl*tkkknqkknqkk---

---XXKKXFFXXPXFFSXKKKPXKXPXKKKKKKKFFFFLXPXXNXPFFPXKKKKKKKL

Frame B:
XTLIVVNCVILNKYYYFVPLLYKQKKKTKKKTKKK---

---xkkkxffxxpxffpxkknpkkxpkkkkkkknffffxpxxktxxffxxkkkkkkn

Frame C:
tl***liv*y*iniiilyhyfinkkkkpkkkpkk---

---xkkxffxxppfffpkkktxkkxxkkkkkkkiffffxpxxkpxxfsxkkkkkkki
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U09800-1 (Contig-U09800-1Q)
/CSM_Contig/Contig-U09800-1Q.Seq.d
         (281 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U09800-1 (Contig-U09800-1Q) /CSM_Contig/Conti...   137  7e-33
Contig-U10382-1 (Contig-U10382-1Q) /CSM_Contig/Conti...    42  3e-04
Contig-U02223-1 (Contig-U02223-1Q) /CSM_Contig/Conti...    42  3e-04
Contig-U14126-1 (Contig-U14126-1Q) /CSM_Contig/Conti...    36  0.019
Contig-U13620-1 (Contig-U13620-1Q) /CSM_Contig/Conti...    36  0.019
Contig-U13007-1 (Contig-U13007-1Q) /CSM_Contig/Conti...    36  0.019
Contig-U11097-1 (Contig-U11097-1Q) /CSM_Contig/Conti...    36  0.019
Contig-U05669-1 (Contig-U05669-1Q) /CSM_Contig/Conti...    36  0.019
Contig-U05649-1 (Contig-U05649-1Q) /CSM_Contig/Conti...    36  0.019
Contig-U13270-1 (Contig-U13270-1Q) /CSM_Contig/Conti...    34  0.075

>Contig-U09800-1 (Contig-U09800-1Q) /CSM_Contig/Contig-U09800-1Q.Seq.d
          Length = 281

 Score =  137 bits (69), Expect = 7e-33
 Identities = 69/69 (100%)
 Strand = Plus / Plus

                                                                      
Query: 3  acactctaatagtagttaattgtgtaatattaaataaatattattattttgtaccattac 62
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 3  acactctaatagtagttaattgtgtaatattaaataaatattattattttgtaccattac 62

                   
Query: 63 tttataaac 71
          |||||||||
Sbjct: 63 tttataaac 71


>Contig-U10382-1 (Contig-U10382-1Q) /CSM_Contig/Contig-U10382-1Q.Seq.d
          Length = 996

 Score = 42.1 bits (21), Expect = 3e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                               
Query: 30 tattaaataaatattattatt 50
          |||||||||||||||||||||
Sbjct: 57 tattaaataaatattattatt 37


>Contig-U02223-1 (Contig-U02223-1Q) /CSM_Contig/Contig-U02223-1Q.Seq.d
          Length = 712

 Score = 42.1 bits (21), Expect = 3e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                
Query: 32  ttaaataaatattattatttt 52
           |||||||||||||||||||||
Sbjct: 705 ttaaataaatattattatttt 685


  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: 5258
Number of Sequences: 6905
Number of extensions: 5258
Number of successful extensions: 2338
Number of sequences better than 10.0: 257
length of query: 281
length of database: 5,674,871
effective HSP length: 15
effective length of query: 266
effective length of database: 5,571,296
effective search space: 1481964736
effective search space used: 1481964736
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 2008.11.18
Homology vs DNA 
Query= Contig-U09800-1 (Contig-U09800-1Q) /CSM_Contig/Contig-U09800-1Q.Seq.d
         (281 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

(AU266271) Dictyostelium discoideum vegetative cDNA clone:VS...   137   2e-28  1
(AL035477) Plasmodium falciparum MAL4P4.                           50   0.041  1
(AL355979) Human DNA sequence from clone RP11-466G24 on chro...    50   0.041  1
(DJ082835) Alteration Of Embryo/Endosperm Size During Seed D...    48   0.16   1
(BX004974) Zebrafish DNA sequence from clone CH211-74A16 in ...    46   0.64   1
(AM451641) Vitis vinifera contig VV78X228114.7, whole genome...    46   0.64   1
(GC515576) Sequence 26 from patent US 7407802.                     46   0.64   1
(GC515575) Sequence 25 from patent US 7407802.                     46   0.64   1
(GC515574) Sequence 24 from patent US 7407802.                     46   0.64   1
(GC515567) Sequence 12 from patent US 7407802.                     46   0.64   1
(EA359034) Sequence 38 from patent US 7288643.                     46   0.64   1
(EA359023) Sequence 27 from patent US 7288643.                     46   0.64   1
(EA359021) Sequence 25 from patent US 7288643.                     46   0.64   1
(EA359020) Sequence 24 from patent US 7288643.                     46   0.64   1
(EA359018) Sequence 22 from patent US 7288643.                     46   0.64   1
(EA072178) Sequence 2 from patent US 7179965.                      46   0.64   1
(EA072177) Sequence 1 from patent US 7179965.                      46   0.64   1
(EA021067) Sequence 26 from patent US 7132291.                     46   0.64   1
(EA021066) Sequence 25 from patent US 7132291.                     46   0.64   1
(EA021065) Sequence 24 from patent US 7132291.                     46   0.64   1
(EA021058) Sequence 12 from patent US 7132291.                     46   0.64   1
(E00546) DNA fragment of T-DNA of Ti-plasmid,pTi15955.             46   0.64   1
(E00404) Ti plasmid T-DNA region.                                  46   0.64   1
(DI139267) Vectors and Cells for Preparing Immunoprotective ...    46   0.64   1
(DI125909) Vectors and Cells for Preparing Immunoprotective ...    46   0.64   1
(DI125256) Vectors and Cells for Preparing Immunoprotective ...    46   0.64   1
(DI124435) Vectors and Cells for Preparing Immunoprotective ...    46   0.64   1
(DD459051) Corn Event TC1507 and Methods for Detection Thereof.    46   0.64   1
(DD459040) Corn Event TC1507 and Methods for Detection Thereof.    46   0.64   1
(DD459038) Corn Event TC1507 and Methods for Detection Thereof.    46   0.64   1
(DD459037) Corn Event TC1507 and Methods for Detection Thereof.    46   0.64   1
(DD459035) Corn Event TC1507 and Methods for Detection Thereof.    46   0.64   1
(CS598021) Sequence 6 from Patent WO2007038345.                    46   0.64   1
(CS195874) Sequence 2 from Patent WO2005103266.                    46   0.64   1
(CS195873) Sequence 1 from Patent WO2005103266.                    46   0.64   1
(CQ945876) Sequence 38 from Patent WO2004099447.                   46   0.64   1
(CQ945865) Sequence 27 from Patent WO2004099447.                   46   0.64   1
(CQ945863) Sequence 25 from Patent WO2004099447.                   46   0.64   1
(CQ945862) Sequence 24 from Patent WO2004099447.                   46   0.64   1
(CQ945860) Sequence 22 from Patent WO2004099447.                   46   0.64   1
(BD251970) Artificial matrix attachment region for increasin...    46   0.64   1
(BD251969) Artificial matrix attachment region for increasin...    46   0.64   1
(BD251968) Artificial matrix attachment region for increasin...    46   0.64   1
(BD244511) Modification of fatty acid composition of plants ...    46   0.64   1
(BD132700) Regulatory sequences for transgenic plants.             46   0.64   1
(BD132699) Regulatory sequences for transgenic plants.             46   0.64   1
(BD132698) Regulatory sequences for transgenic plants.             46   0.64   1
(BD016312) Method of promoting plant transcription by using ...    46   0.64   1
(AR482072) Sequence 10 from patent US 6699984.                     46   0.64   1
(AR482071) Sequence 9 from patent US 6699984.                      46   0.64   1
(AR482070) Sequence 8 from patent US 6699984.                      46   0.64   1
(AR364803) Sequence 1 from patent US 5428147.                      46   0.64   1
(AR267509) Sequence 11 from patent US 6495738.                     46   0.64   1
(AR209003) Sequence 10 from patent US 6384207.                     46   0.64   1
(AR209002) Sequence 9 from patent US 6384207.                      46   0.64   1
(AR209001) Sequence 8 from patent US 6384207.                      46   0.64   1
(CU695208) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    46   0.64   1
(AP008071) Lotus japonicus genomic DNA, chromosome 5, clone:...    46   0.64   1
(AC200256) Zea mays chromosome 1 clone CH201-24M2; ZMMBBc002...    46   0.64   1
(AC186905) Zea mays chromosome 1 clone CH201-247I6; ZMMBBc02...    46   0.64   1
(CZ901755) ugma002f003e10f0 Soybean methylation unfiltered l...    46   0.64   1
(CC699547) OGVBQ79TH ZM_0.7_1.5_KB Zea mays genomic clone ZM...    46   0.64   1
(CC062860) ugma002f003e10f0 ugma unfiltered library (LibID: ...    46   0.64   1
(BZ365749) ie28g08.g1 WGS-ZmaysF (JM107 adapted methyl filte...    46   0.64   1
(BZ362067) ie28g08.b1 WGS-ZmaysF (JM107 adapted methyl filte...    46   0.64   1
(DY223834) ID0AAI1YG11RM1 ID0AEE Acyrthosiphon pisum cDNA cl...    46   0.64   1
(X00493) Agrobacterium tumefaciens Ti plasmid pTi15955 T-DNA...    46   0.64   1
(AF242881) Agrobacterium tumefaciens octopine-type Ti plasmi...    46   0.64   1
(CU302358) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    42   1.5    2
(CU457815) Zebrafish DNA sequence from clone CH211-12K12 in ...    44   2.5    1
(CR848668) Zebrafish DNA sequence from clone DKEY-82O10 in l...    44   2.5    1
(BX284672) Zebrafish DNA sequence from clone DKEY-88N24 in l...    44   2.5    1
(BX248137) Zebrafish DNA sequence from clone DKEY-19L19.           44   2.5    1
(AP010322) Lotus japonicus genomic DNA, chromosome 1, clone:...    44   2.5    1
(AP004923) Lotus japonicus genomic DNA, chromosome 1, clone:...    44   2.5    1
(AB331278) Syngonium podophyllum chloroplast rpl2, trnH, psb...    44   2.5    1
(AR553950) Sequence 9081 from patent US 6747137.                   44   2.5    1
(AY037525) Euaresta aequalis 16S ribosomal RNA gene, partial...    44   2.5    1
(AC000055) Human PAC clone DJ073F11 from Xq23, complete sequ...    44   2.5    1
(CU861901) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   2.5    1
(CT573355) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   2.5    1
(AF257499) Homo sapiens chromosome 8 clone GS1-179c23 map 8p...    44   2.5    1
(AC221619) Bos taurus clone CH240-391A10, WORKING DRAFT SEQU...    44   2.5    1
(AC220859) Bos taurus clone CH240-343A1, WORKING DRAFT SEQUE...    44   2.5    1
(AC208897) Zea mays chromosome 1 clone CH201-141M18; ZMMBBc0...    44   2.5    1
(AC196471) Zea mays chromosome 1 clone ZMMBBb-271K21; ZMMBBb...    44   2.5    1
(AC189800) Zea mays chromosome 10 clone CH201-124J20; ZMMBBc...    44   2.5    1
(AC167106) Sorex araneus clone SA_Ba-359B10, WORKING DRAFT S...    44   2.5    1
(BH135551) ENTOO30TF Entamoeba histolytica Sheared DNA Entam...    44   2.5    1
(EK583876) 1095522019462 Global-Ocean-Sampling_GS-32-01-01-1...    44   2.5    1
(EK571306) 1095521079188 Global-Ocean-Sampling_GS-32-01-01-1...    44   2.5    1
(EK122524) 1092964602623 Global-Ocean-Sampling_GS-31-01-01-1...    44   2.5    1
(EK075085) 1092961025933 Global-Ocean-Sampling_GS-31-01-01-1...    44   2.5    1
(EK068362) 1092960155166 Global-Ocean-Sampling_GS-31-01-01-1...    44   2.5    1
(EK060608) 1092960075975 Global-Ocean-Sampling_GS-31-01-01-1...    44   2.5    1
(EJ973792) 1093022101389 Global-Ocean-Sampling_GS-30-02-01-1...    44   2.5    1
(EJ942979) 1093018897416 Global-Ocean-Sampling_GS-30-02-01-1...    44   2.5    1
(EJ594189) 1092961068476 Global-Ocean-Sampling_GS-29-01-01-1...    44   2.5    1
(EJ150372) 1092343755567 Global-Ocean-Sampling_GS-27-01-01-1...    44   2.5    1
(DE579304) Bombyx mori genomic DNA, Fosmid clone:GBMFno228_d...    44   2.5    1

>(AU266271) Dictyostelium discoideum vegetative cDNA clone:VSG302,
          5' end single read.
          Length = 107

 Score =  137 bits (69), Expect = 2e-28
 Identities = 69/69 (100%)
 Strand = Plus / Plus


Query: 3  acactctaatagtagttaattgtgtaatattaaataaatattattattttgtaccattac 62
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 3  acactctaatagtagttaattgtgtaatattaaataaatattattattttgtaccattac 62


Query: 63 tttataaac 71
          |||||||||
Sbjct: 63 tttataaac 71

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 119,834,462
Number of extensions: 9934197
Number of successful extensions: 1078792
Number of sequences better than 10.0: 176
Length of query: 281
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 258
Effective length of database: 93,106,754,628
Effective search space: 24021542694024
Effective search space used: 24021542694024
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.26
Homology vs Protein 
Query= Contig-U09800-1 (Contig-U09800-1Q) /CSM_Contig/Contig-U09800-1Q.Seq.d
         (281 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 105,551,097
Number of extensions: 658216
Number of successful extensions: 1618
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1581
Number of HSP's successfully gapped: 0
Length of query: 93
Length of database: 1,040,966,779
Length adjustment: 62
Effective length of query: 31
Effective length of database: 842,301,109
Effective search space: 26111334379
Effective search space used: 26111334379
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: 0.90  gvh: 0.28  alm: 0.39  top: 0.80  tms: 0.00  mit: 0.40  mip: 0.00
 nuc: 0.92  erl: 0.00  erm: 0.80  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
	 20.0 %: cytoplasmic
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U09800-1 is nuc
VS (DIR, S) 1
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) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0