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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-U15501-1
Contig ID Contig-U15501-1
Contig update 2004. 6.11
Contig sequence 
>Contig-U15501-1 (Contig-U15501-1Q) /CSM_Contig/Contig-U15501-1Q.Seq.d
CTGGGTACCCGGGCCCCCCCTCGNGGTCGACCCACGCCGTCCGCAAGATA
TTTTACACAAATAAAATATTTAAACATATTAAAACAAACAAATAAATAAA
ATAAAATAATTAATTAAATATATATATATCAGTTTTTTTTTTTCATTACA
ATATATTAAAAAAAAAA
Gap no gap
Contig length 167
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 1084551
End point 1084429
Strand (PLUS/MINUS) MINUS
Number of clones 7
Number of EST 7
Link to clone list U15501
List of clone(s) 

est1=VSJ323F,1,167
est2=VSJ864F,24,167
est3=VSF834F,45,167
est4=VSG639F,45,167
est5=VSI555F,45,167
est6=VSF346F,48,167
est7=VSK172F,49,167
Translated Amino Acid sequence 
LGTRAPPRGRPTPSARYFTQIKYLNILKQTNK*nkiin*iyiyqffffitiy*kk
Translated Amino Acid sequence (All Frames) 
Frame A:
LGTRAPPRGRPTPSARYFTQIKYLNILKQTNK*nkiin*iyiyqffffitiy*kk


Frame B:
wvpgpplxvdprrpqdilhk*ni*ty*nkqinkik*likyiyisfffslqyikkk


Frame C:
gypgppsxsthavrkifytnkifkhiktnk*ik*nn*lniyisvfffhynilkkk
own update 2004. 6.23
Homology vs CSM-cDNA 
Query= Contig-U15501-1 (Contig-U15501-1Q)
/CSM_Contig/Contig-U15501-1Q.Seq.d
         (167 letters)

Database: CSM
           8402 sequences; 8,075,542 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U15501-1 (Contig-U15501-1Q) /CSM_Contig/Conti...    62  3e-10
Contig-U13869-1 (Contig-U13869-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U04920-1 (Contig-U04920-1Q) /CSM_Contig/Conti...    36  0.016
Contig-U03807-1 (Contig-U03807-1Q) /CSM_Contig/Conti...    36  0.016
Contig-U01901-1 (Contig-U01901-1Q) /CSM_Contig/Conti...    34  0.062
Contig-U06577-1 (Contig-U06577-1Q) /CSM_Contig/Conti...    32  0.24
Contig-U16460-1 (Contig-U16460-1Q) /CSM_Contig/Conti...    30  0.96
Contig-U16424-1 (Contig-U16424-1Q) /CSM_Contig/Conti...    30  0.96
Contig-U16275-1 (Contig-U16275-1Q) /CSM_Contig/Conti...    30  0.96
Contig-U16220-1 (Contig-U16220-1Q) /CSM_Contig/Conti...    30  0.96

>Contig-U15501-1 (Contig-U15501-1Q) /CSM_Contig/Contig-U15501-1Q.Seq.d
          Length = 167

 Score = 61.9 bits (31), Expect = 3e-10
 Identities = 34/34 (100%)
 Strand = Plus / Plus

                                            
Query: 21 tcgnggtcgacccacgccgtccgcaagatatttt 54
          ||||||||||||||||||||||||||||||||||
Sbjct: 21 tcgnggtcgacccacgccgtccgcaagatatttt 54


 Score = 36.2 bits (18), Expect = 0.016
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 115 taaatatatatatatcag 132
           ||||||||||||||||||
Sbjct: 115 taaatatatatatatcag 132


 Score = 28.2 bits (14), Expect = 3.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 144 cattacaatatatt 157
           ||||||||||||||
Sbjct: 144 cattacaatatatt 157


>Contig-U13869-1 (Contig-U13869-1Q) /CSM_Contig/Contig-U13869-1Q.Seq.d
          Length = 550

 Score = 40.1 bits (20), Expect = 0.001
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                 
Query: 21 tcgnggtcgacccacgccgtccg 43
          ||| |||||||||||||||||||
Sbjct: 20 tcgaggtcgacccacgccgtccg 42


>Contig-U04920-1 (Contig-U04920-1Q) /CSM_Contig/Contig-U04920-1Q.Seq.d
          Length = 429

 Score = 36.2 bits (18), Expect = 0.016
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                            
Query: 26 gtcgacccacgccgtccg 43
          ||||||||||||||||||
Sbjct: 10 gtcgacccacgccgtccg 27


  Database: CSM
    Posted date:  Jun 21, 2004  1:35 PM
  Number of letters in database: 8,075,542
  Number of sequences in database:  8402
  
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: 3096
Number of Sequences: 8402
Number of extensions: 3096
Number of successful extensions: 1755
Number of sequences better than 10.0: 206
length of query: 167
length of database: 8,075,542
effective HSP length: 15
effective length of query: 152
effective length of database: 7,949,512
effective search space: 1208325824
effective search space used: 1208325824
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. 1.29
Homology vs DNA 
Query= Contig-U15501-1 (Contig-U15501-1Q) /CSM_Contig/Contig-U15501-1Q.Seq.d
         (167 letters)

Database: ddbj_B
           98,226,423 sequences; 98,766,808,389 total letters

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

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(AU269750) Dictyostelium discoideum vegetative cDNA clone:VS...    66   2e-12  3
(ES287693) PR013G02.XT7 nitrogen starvation culture of P. br...    46   0.37   1
(CO442538) MZCCL10045A07.g Maize Endosperm cDNA Library Zea ...    46   0.37   1
(BX846921) RZPD Xenopus laevis cDNA clone IMAGp998G0114198 =...    46   0.37   1
(BU068192) 2555_C08_E15ZT5 Mature perithecia Gibberella zeae...    40   1.0    2
(AM941134) Hordeum vulgare subsp. vulgare partial mRNA for p...    44   1.5    1
(EG364972) chan00547 Leaf of wild-type tomato cDNA library S...    44   1.5    1
(CO969706) BeG120N10E01 BeG120N Blastocladiella emersonii cD...    44   1.5    1
(CO452825) MZCCL10186B06.g Maize Endosperm cDNA Library Zea ...    44   1.5    1
(CO446280) MZCCL10094H01.g Maize Endosperm cDNA Library Zea ...    44   1.5    1
(CO445763) MZCCL10088H07.g Maize Endosperm cDNA Library Zea ...    44   1.5    1
(CD878374) AZO4.102J17F011002 AZO4 Triticum aestivum cDNA cl...    44   1.5    1
(BQ764928) EBca01_SQ005_E10 _R carpel, pre-anthesis, no trea...    44   1.5    1
(BQ762725) EBro02_SQ004_J24 _R root, 3 week, hydroponic grow...    44   1.5    1
(EY719394) CS00-C3-702-089-F07-CT.F Sweet orange fruit, deve...    44   1.5    1
(AU266951) Dictyostelium discoideum vegetative cDNA clone:VS...    34   3.6    2
(EV146753) 0212687 Brassica napus Very early anther Brassica...    34   3.9    2
(BX842595) Neurospora crassa DNA linkage group II BAC clone ...    42   5.9    1
(ES551886) TL2005D04SP6 TL2 Tribolium castaneum cDNA, mRNA s...    42   5.9    1
(ES550057) TH1019B05SP6 TH1 Tribolium castaneum cDNA, mRNA s...    42   5.9    1
(ES549970) TH1018G10SP6 TH1 Tribolium castaneum cDNA, mRNA s...    42   5.9    1
(ES549829) TH1017H06SP6 TH1 Tribolium castaneum cDNA, mRNA s...    42   5.9    1
(ES549649) TH1016D06SP6 TH1 Tribolium castaneum cDNA, mRNA s...    42   5.9    1
(ES548449) TH1002B11SP6 TH1 Tribolium castaneum cDNA, mRNA s...    42   5.9    1
(ES288059) PR029C04.XT7 nitrogen starvation culture of P. br...    42   5.9    1
(DW705548) EST029029 Trichophyton rubrum cDNA library 7 Tric...    42   5.9    1
(DN615940) SPM2C6 Saprolegnia parasitica ATCC90214 mycelium ...    42   5.9    1
(DN439157) LIB4284-001-Q1-K1-A9 LIB4284 Canis lupus familiar...    42   5.9    1
(DN438875) LIB4282-001-Q1-K1-B2 LIB4282 Canis lupus familiar...    42   5.9    1
(CV667007) LCPE04EX020059A11.g Exponential growth phase Leis...    42   5.9    1
(CO452866) MZCCL10186G04.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO450977) MZCCL10156F06.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO449639) MZCCL10141D02.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO446917) MZCCL10113C01.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO446537) MZCCL10110C05.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO446274) MZCCL10094G05.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO446159) MZCCL10093C02.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO444405) MZCCL10071B09.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO443469) MZCCL10057F10.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO442976) MZCCL10058B04.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CO442968) MZCCL10058A05.g Maize Endosperm cDNA Library Zea ...    42   5.9    1
(CJ376049) Molgula tectiformis cDNA, gastrula/neurula clone:...    42   5.9    1
(CF284590) AGENCOURT_15206757 NICHD_XGC_Sp1 Xenopus laevis c...    42   5.9    1
(CD910097) G468.114G10F010821 G468 Triticum aestivum cDNA cl...    42   5.9    1
(CD899746) G174.113H01F010827 G174 Triticum aestivum cDNA cl...    42   5.9    1
(BQ766521) EBro08_SQ006_G09 _R root, 3 week, drought-stresse...    42   5.9    1
(BQ762993) EBro02_SQ006_F20_R root, 3 week, hydroponic grown...    42   5.9    1
(BQ760216) EBpi07_SQ003_E17 _R pistil, 12 DPA, no treatment,...    42   5.9    1
(BQ430719) AGENCOURT_7766516 NIH_MGC_68 Homo sapiens cDNA cl...    42   5.9    1
(EY875786) CL06-C4-501-042-E09-CT.F Rangpur lime root, plant...    42   5.9    1
(EY658739) CS00-C1-100-138-G10-CT.F Sweet orange leaf, green...    42   5.9    1

>(AU269750) Dictyostelium discoideum vegetative cDNA clone:VSJ323,
          5' end single read.
          Length = 167

 Score = 65.9 bits (33), Expect(3) = 2e-12
 Identities = 36/36 (100%)
 Strand = Plus / Plus


Query: 21 tcgnggtcgacccacgccgtccgcaagatattttac 56
          ||||||||||||||||||||||||||||||||||||
Sbjct: 21 tcgnggtcgacccacgccgtccgcaagatattttac 56

 Score = 28.2 bits (14), Expect(3) = 2e-12
 Identities = 14/14 (100%)
 Strand = Plus / Plus


Query: 144 cattacaatatatt 157
           ||||||||||||||
Sbjct: 144 cattacaatatatt 157

 Score = 26.3 bits (13), Expect(3) = 2e-12
 Identities = 13/13 (100%)
 Strand = Plus / Plus


Query: 1  ctgggtacccggg 13
          |||||||||||||
Sbjct: 1  ctgggtacccggg 13

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 98226423
Number of Hits to DB: 34,418,429
Number of extensions: 1996357
Number of successful extensions: 503120
Number of sequences better than 10.0: 55
Length of query: 167
Length of database: 98,766,808,389
Length adjustment: 22
Effective length of query: 145
Effective length of database: 96,605,827,083
Effective search space: 14007844927035
Effective search space used: 14007844927035
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.16
Homology vs Protein 
Query= Contig-U15501-1 (Contig-U15501-1Q) /CSM_Contig/Contig-U15501-1Q.Seq.d
         (167 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: 169,445,421
Number of extensions: 1917722
Number of successful extensions: 1567
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1566
Number of HSP's successfully gapped: 0
Length of query: 55
Length of database: 1,051,180,864
Length adjustment: 28
Effective length of query: 27
Effective length of database: 960,557,212
Effective search space: 25935044724
Effective search space used: 25935044724
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: 26 (14.6 bits)
PSORT 

 psg: 0.69  gvh: 0.11  alm: 0.62  top: 0.53  tms: 0.00  mit: 0.62  mip: 0.00
 nuc: 0.12  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 

	 48.0 %: mitochondrial
	 32.0 %: nuclear
	 12.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U15501-1 is mit
VS (DIR, S) 7
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