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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-U11859-1
Contig ID Contig-U11859-1
Contig update 2002.12.18
Contig sequence 
>Contig-U11859-1 (Contig-U11859-1Q) /CSM_Contig/Contig-U11859-1Q.Seq.d
ATTTTATTTTTTTATTTTAAAATATCTGAATCCTGCAAAAATAATCTGAT
TTTTATATTTTTTGATTATATTTTTTAATATGTGTTGTCCCAAGGTTAAC
CAAATAAAAAGATTTAAAAATAATTTGGTTAATAATAAAAATTAATTGGT
AATAAAAAAAAATATAAAATAAAAAAAAACCCAATTTAATAATTTATTAA
TTTTATAAAAAAAAAAATTATANNNNNNNNN----------TGGATCTCA
ATTCATTAATAATACCCGCAGCAGTTAGTGGTGGTGCAATTGATATCTAC
TCAAGTAGTATAACTATTAACAGTACTAGCTTCATTGGAAACTATGCTAA
ACAAGATGATCATGGTCCTTCAGTTTATTGTACAAACTCTAAAATTAACC
TTTCAAGTACTACTTTTAAAATTAATGAAACCAATACTGTAAATTCTTTT
GGTATAGATTGCTTACCATCAGTTTCATATTTTTGTACTGTTATTAATCA
ATCTAAAAAATTACAATGTGAAAAAGATGATTTCGAAATCTCTAGTGATA
ATACAAACGGATTAACAACTGGTCAAAAAGTTGGAATTTCATTTGGTGTC
ATTGGTGGATTTTTCTTAATTGTTATAGTTGCAGTTTTAGTTGTTAGAAA
AGTTAAAAGAGATAGACAATATAAACCAATTGGTTTATAATAAAAATAAT
AAATAAATTTATTCAAATTATTATTTTTTTATTTATTTAAAAAAGATTAA
ATTTTATTTATTTATTTTATTGTATATTATGTTATTTATTNATTTATTTA
NTTATTTATTTATNTATGTANTATTTTC
Gap gap included
Contig length 818
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 2
Number of EST 3
Link to clone list U11859
List of clone(s) 

est1=CHM857F,1,222
est2=SSA268Z,223,724
est3=CHM857Z,418,810
Translated Amino Acid sequence 
ilffyfkisescknnlififfdyif*yvlsqg*pnkki*k*fg***klignkkkykikkn
pi**FINFIKKKIIXXX---

---DLNSLIIPAAVSGGAIDIYSSSITINSTSFIGNYAKQDDHGPSVYCTNSKINLSSTT
FKINETNTVNSFGIDCLPSVSYFCTVINQSKKLQCEKDDFEISSDNTNGLTTGQKVGISF
GVIGGFFLIVIVAVLVVRKVKRDRQYKPIGL**k**inlfkllffylfkkd*ilfiyfiv
yyviyxfixlfiyxcxif
Translated Amino Acid sequence (All Frames) 
Frame A:
ilffyfkisescknnlififfdyif*yvlsqg*pnkki*k*fg***klignkkkykikkn
pi**FINFIKKKIIXXX---

---wisih**ypqqlvvvqlistqvv*lltvlasletmlnkmimvlqfivqtlkltfqvl
llklmkpil*illv*iayhqfhifvlllinlknynvkkmiskslviiqtd*qlvkklefh
lvslvdfs*ll*lqf*lleklkeidninqlvynknnk*iysnyyffiylkkikfylfill
yimlfixlfxylfxyvxf

Frame B:
fyffilkylnpakii*flyfliiffnmccpkvnqikrfknnlvnnkn*lvikknik*kkt
qfnnllil*kkklxxx---

---gsqfinntrss*wwcn*yllk*yny*qy*lhwklc*tr*swsfsllykl*n*pfkyy
f*n**nqyckffwyrlltisfiflycy*si*kitm*kr*frnl***ykrinnwskswnfi
wchwwiflncyscsfsc*ks*kr*ti*tnwfiikiinkfiqiiiflfi*krlnfiylfyc
ilcylxiylxiylxmxyf

Frame C:
fiflf*ni*ilqk*sdfyif*lyflicvvprltk*kdlkiiwliikinw**kki*nkkkp
nliiy*fykkknyxxx---

---DLNSLIIPAAVSGGAIDIYSSSITINSTSFIGNYAKQDDHGPSVYCTNSKINLSSTT
FKINETNTVNSFGIDCLPSVSYFCTVINQSKKLQCEKDDFEISSDNTNGLTTGQKVGISF
GVIGGFFLIVIVAVLVVRKVKRDRQYKPIGL**k**inlfkllffylfkkd*ilfiyfiv
yyviyxfixlfiyxcxif
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U11859-1 (Contig-U11859-1Q)
/CSM_Contig/Contig-U11859-1Q.Seq.d
         (828 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U11859-1 (Contig-U11859-1Q) /CSM_Contig/Conti...   839  0.0
Contig-U02000-1 (Contig-U02000-1Q) /CSM_Contig/Conti...    42  0.001
Contig-U01725-1 (Contig-U01725-1Q) /CSM_Contig/Conti...    40  0.004
Contig-U13794-1 (Contig-U13794-1Q) /CSM_Contig/Conti...    38  0.015
Contig-U11176-1 (Contig-U11176-1Q) /CSM_Contig/Conti...    38  0.015
Contig-U11052-1 (Contig-U11052-1Q) /CSM_Contig/Conti...    38  0.015
Contig-U01940-1 (Contig-U01940-1Q) /CSM_Contig/Conti...    38  0.015
Contig-U12590-1 (Contig-U12590-1Q) /CSM_Contig/Conti...    36  0.058
Contig-U01103-1 (Contig-U01103-1Q) /CSM_Contig/Conti...    36  0.058
Contig-U14379-1 (Contig-U14379-1Q) /CSM_Contig/Conti...    34  0.23

>Contig-U11859-1 (Contig-U11859-1Q) /CSM_Contig/Contig-U11859-1Q.Seq.d
          Length = 828

 Score =  839 bits (423), Expect = 0.0
 Identities = 423/423 (100%)
 Strand = Plus / Plus

                                                                       
Query: 242 tggatctcaattcattaataatacccgcagcagttagtggtggtgcaattgatatctact 301
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 242 tggatctcaattcattaataatacccgcagcagttagtggtggtgcaattgatatctact 301

                                                                       
Query: 302 caagtagtataactattaacagtactagcttcattggaaactatgctaaacaagatgatc 361
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 302 caagtagtataactattaacagtactagcttcattggaaactatgctaaacaagatgatc 361

                                                                       
Query: 362 atggtccttcagtttattgtacaaactctaaaattaacctttcaagtactacttttaaaa 421
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 362 atggtccttcagtttattgtacaaactctaaaattaacctttcaagtactacttttaaaa 421

                                                                       
Query: 422 ttaatgaaaccaatactgtaaattcttttggtatagattgcttaccatcagtttcatatt 481
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 422 ttaatgaaaccaatactgtaaattcttttggtatagattgcttaccatcagtttcatatt 481

                                                                       
Query: 482 tttgtactgttattaatcaatctaaaaaattacaatgtgaaaaagatgatttcgaaatct 541
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 482 tttgtactgttattaatcaatctaaaaaattacaatgtgaaaaagatgatttcgaaatct 541

                                                                       
Query: 542 ctagtgataatacaaacggattaacaactggtcaaaaagttggaatttcatttggtgtca 601
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 542 ctagtgataatacaaacggattaacaactggtcaaaaagttggaatttcatttggtgtca 601

                                                                       
Query: 602 ttggtggatttttcttaattgttatagttgcagttttagttgttagaaaagttaaaagag 661
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 602 ttggtggatttttcttaattgttatagttgcagttttagttgttagaaaagttaaaagag 661

              
Query: 662 ata 664
           |||
Sbjct: 662 ata 664


 Score = 54.0 bits (27), Expect = 2e-07
 Identities = 27/27 (100%)
 Strand = Plus / Plus

                                      
Query: 180 cccaatttaataatttattaattttat 206
           |||||||||||||||||||||||||||
Sbjct: 180 cccaatttaataatttattaattttat 206


 Score = 50.1 bits (25), Expect = 4e-06
 Identities = 25/25 (100%)
 Strand = Plus / Plus

                                    
Query: 77  aatatgtgttgtcccaaggttaacc 101
           |||||||||||||||||||||||||
Sbjct: 77  aatatgtgttgtcccaaggttaacc 101


>Contig-U02000-1 (Contig-U02000-1Q) /CSM_Contig/Contig-U02000-1Q.Seq.d
          Length = 1721

 Score = 42.1 bits (21), Expect = 0.001
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                 
Query: 184  atttaataatttattaatttt 204
            |||||||||||||||||||||
Sbjct: 1655 atttaataatttattaatttt 1635


 Score = 30.2 bits (15), Expect = 3.6
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                           
Query: 192  atttattaattttat 206
            |||||||||||||||
Sbjct: 1686 atttattaattttat 1672


>Contig-U01725-1 (Contig-U01725-1Q) /CSM_Contig/Contig-U01725-1Q.Seq.d
          Length = 537

 Score = 40.1 bits (20), Expect = 0.004
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 184 atttaataatttattaattt 203
           ||||||||||||||||||||
Sbjct: 435 atttaataatttattaattt 454


  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: 8583
Number of Sequences: 6905
Number of extensions: 8583
Number of successful extensions: 1047
Number of sequences better than 10.0: 133
length of query: 828
length of database: 5,674,871
effective HSP length: 16
effective length of query: 812
effective length of database: 5,564,391
effective search space: 4518285492
effective search space used: 4518285492
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 2008.11.27
Homology vs DNA 
Query= Contig-U11859-1 (Contig-U11859-1Q) /CSM_Contig/Contig-U11859-1Q.Seq.d
         (828 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

(C25611) Dictyostelium discoideum slug cDNA, clone SSA268.        805   0.0    1
(BJ383865) Dictyostelium discoideum cDNA clone:ddc47b16, 3' ...   188   7e-69  2
(BA000016) Clostridium perfringens str. 13 DNA, complete gen...    52   0.034  1
(BJ368635) Dictyostelium discoideum cDNA clone:ddc47b16, 5' ...    50   0.13   1
(CU693495) Zebrafish DNA sequence from clone DKEY-6M13 in li...    46   2.1    1
(EI301235) GM_WBc0027I18.r GM_WBc Glycine max genomic clone ...    46   2.1    1
(AL721200) Danio rerio embryonic inner ear subtracted cDNA l...    46   2.1    1
(AI544892) fb69f06.x1 Zebrafish WashU MPIMG EST Danio rerio ...    46   2.1    1
(AX590980) Sequence 420 from Patent WO02086113.                    44   8.3    1
(AC107387) Homo sapiens BAC clone RP11-321I11 from 2, comple...    44   8.3    1
(AC104074) Homo sapiens chromosome UNK clone RP11-370G4, WOR...    44   8.3    1
(EK259969) 1095462116720 Global-Ocean-Sampling_GS-31-01-01-1...    44   8.3    1
(EK246446) 1095460259578 Global-Ocean-Sampling_GS-31-01-01-1...    44   8.3    1
(EI870413) CAH1-35J8TV CAA1Ba Cicer arietinum genomic clone ...    44   8.3    1
(DY292958) IC0AAA81BG01RM1 CitNFL Citrus clementina cDNA 5',...    44   8.3    1
(DY287623) IC0AAA68BD10RM1 CitNFL Citrus clementina cDNA 5',...    44   8.3    1
(DY286736) IC0AAA65DE03RM1 CitNFL Citrus clementina cDNA 5',...    44   8.3    1
(DY269772) IC0AAA27DE02RM1 CitNFL Citrus clementina cDNA 5',...    44   8.3    1
(CF507756) USDA-FP_123000-257 Immature Ovaries from field-co...    44   8.3    1
(CA295645) SCRLLV1025D02.b LV1 Saccharum officinarum cDNA cl...    44   8.3    1
(BP954448) Euphorbia tirucalli mRNA, clone: ETC025B11, 5' end.     44   8.3    1
(EY879421) LT33-C1-003-032-H04-CT.F Tahiti lime leaf, greenh...    44   8.3    1
(EY840986) PT11-C9-005-034-C05-CT.F Poncirus trifoliata seed...    44   8.3    1
(EY800827) CR05-C3-701-043-G12-CT.F Mandarin fruit, developm...    44   8.3    1
(EY800747) CR05-C3-701-100-H08-CT.F Mandarin fruit, developm...    44   8.3    1

>(C25611) Dictyostelium discoideum slug cDNA, clone SSA268.
          Length = 502

 Score =  805 bits (406), Expect = 0.0
 Identities = 406/406 (100%)
 Strand = Plus / Plus


Query: 242 tggatctcaattcattaataatacccgcagcagttagtggtggtgcaattgatatctact 301
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   tggatctcaattcattaataatacccgcagcagttagtggtggtgcaattgatatctact 60


Query: 302 caagtagtataactattaacagtactagcttcattggaaactatgctaaacaagatgatc 361
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  caagtagtataactattaacagtactagcttcattggaaactatgctaaacaagatgatc 120


Query: 362 atggtccttcagtttattgtacaaactctaaaattaacctttcaagtactacttttaaaa 421
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 atggtccttcagtttattgtacaaactctaaaattaacctttcaagtactacttttaaaa 180


Query: 422 ttaatgaaaccaatactgtaaattcttttggtatagattgcttaccatcagtttcatatt 481
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ttaatgaaaccaatactgtaaattcttttggtatagattgcttaccatcagtttcatatt 240


Query: 482 tttgtactgttattaatcaatctaaaaaattacaatgtgaaaaagatgatttcgaaatct 541
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tttgtactgttattaatcaatctaaaaaattacaatgtgaaaaagatgatttcgaaatct 300


Query: 542 ctagtgataatacaaacggattaacaactggtcaaaaagttggaatttcatttggtgtca 601
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 ctagtgataatacaaacggattaacaactggtcaaaaagttggaatttcatttggtgtca 360


Query: 602 ttggtggatttttcttaattgttatagttgcagttttagttgttag 647
           ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 ttggtggatttttcttaattgttatagttgcagttttagttgttag 406

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 520,250,381
Number of extensions: 31075841
Number of successful extensions: 2480119
Number of sequences better than 10.0: 25
Length of query: 828
Length of database: 95,242,211,685
Length adjustment: 24
Effective length of query: 804
Effective length of database: 97,308,875,965
Effective search space: 78236336275860
Effective search space used: 78236336275860
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7. 1
Homology vs Protein 
Query= Contig-U11859-1 (Contig-U11859-1Q) /CSM_Contig/Contig-U11859-1Q.Seq.d
         (828 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: 695,360,111
Number of extensions: 10324191
Number of successful extensions: 21526
Number of sequences better than 10.0: 0
Number of HSP's gapped: 21523
Number of HSP's successfully gapped: 0
Length of query: 276
Length of database: 1,051,180,864
Length adjustment: 127
Effective length of query: 149
Effective length of database: 640,137,871
Effective search space: 95380542779
Effective search space used: 95380542779
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: 32 (16.9 bits)
PSORT 

 psg: 0.70  gvh: 0.51  alm: 0.12  top: 0.93  tms: 0.07  mit: 0.22  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: 1.00  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: 1.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 24.0 %: cytoplasmic
	 20.0 %: nuclear
	 16.0 %: vesicles of secretory system
	 12.0 %: mitochondrial
	  8.0 %: Golgi
	  8.0 %: endoplasmic reticulum
	  4.0 %: extracellular, including cell wall
	  4.0 %: cytoskeletal
	  4.0 %: plasma membrane

>> prediction for Contig-U11859-1 is cyt
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) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0