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Dicty_cDB
Contig List | Clone List | cDNA Library List
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U14430-1
Contig ID Contig-U14430-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14430-1 (Contig-U14430-1Q) /CSM_Contig/Contig-U14430-1Q.Seq.d
ATACCACTTTCAAACAAAAGGAACAAATAATAATAATAATTGTATCAATA
ACCAATAGAATTAATTTTTTTTTTTTTTTTTTNAAAAACTTTAACTTTTT
TNGGAANNNNNNNNN
Gap no gap
Contig length 115
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 4480055
End point 4480160
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U14430
List of clone(s) 

est1=CHO484F,1,106
Translated Amino Acid sequence 
TTFKQKEQIIIIIVSITNRINFFFFFXKNFNFFXXXX
Translated Amino Acid sequence (All Frames) 
Frame A:
iplsnkrnk****lyq*pielifffffxktltfxgxxx


Frame B:
yhfqtkgtnnnnncinnq*n*ffffffxkl*lfxexxx


Frame C:
TTFKQKEQIIIIIVSITNRINFFFFFXKNFNFFXXXX
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14430-1 (Contig-U14430-1Q)
/CSM_Contig/Contig-U14430-1Q.Seq.d
         (115 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14430-1 (Contig-U14430-1Q) /CSM_Contig/Conti...   127  3e-30
Contig-U09201-1 (Contig-U09201-1Q) /CSM_Contig/Conti...    40  5e-04
Contig-U14745-1 (Contig-U14745-1Q) /CSM_Contig/Conti...    38  0.002
Contig-U13937-1 (Contig-U13937-1Q) /CSM_Contig/Conti...    38  0.002
Contig-U13845-1 (Contig-U13845-1Q) /CSM_Contig/Conti...    38  0.002
Contig-U12923-1 (Contig-U12923-1Q) /CSM_Contig/Conti...    38  0.002
Contig-U12546-1 (Contig-U12546-1Q) /CSM_Contig/Conti...    38  0.002
Contig-U12521-1 (Contig-U12521-1Q) /CSM_Contig/Conti...    38  0.002
Contig-U12387-1 (Contig-U12387-1Q) /CSM_Contig/Conti...    38  0.002
Contig-U12276-1 (Contig-U12276-1Q) /CSM_Contig/Conti...    38  0.002

>Contig-U14430-1 (Contig-U14430-1Q) /CSM_Contig/Contig-U14430-1Q.Seq.d
          Length = 115

 Score =  127 bits (64), Expect = 3e-30
 Identities = 64/64 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  ataccactttcaaacaaaaggaacaaataataataataattgtatcaataaccaatagaa 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  ataccactttcaaacaaaaggaacaaataataataataattgtatcaataaccaatagaa 60

              
Query: 61 ttaa 64
          ||||
Sbjct: 61 ttaa 64


 Score = 40.1 bits (20), Expect = 5e-04
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                  
Query: 84  aaaaactttaacttttttnggaa 106
           |||||||||||||||||||||||
Sbjct: 84  aaaaactttaacttttttnggaa 106


>Contig-U09201-1 (Contig-U09201-1Q) /CSM_Contig/Contig-U09201-1Q.Seq.d
          Length = 602

 Score = 40.1 bits (20), Expect = 5e-04
 Identities = 26/28 (92%)
 Strand = Plus / Plus

                                       
Query: 23  acaaataataataataattgtatcaata 50
           |||||||||||||||||| |||| ||||
Sbjct: 231 acaaataataataataatagtattaata 258


>Contig-U14745-1 (Contig-U14745-1Q) /CSM_Contig/Contig-U14745-1Q.Seq.d
          Length = 1780

 Score = 38.2 bits (19), Expect = 0.002
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 22  aacaaataataataataat 40
           |||||||||||||||||||
Sbjct: 724 aacaaataataataataat 742


 Score = 30.2 bits (15), Expect = 0.45
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 26  aataataataataat 40
           |||||||||||||||
Sbjct: 731 aataataataataat 745


 Score = 30.2 bits (15), Expect = 0.45
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 26  aataataataataat 40
           |||||||||||||||
Sbjct: 149 aataataataataat 163


 Score = 30.2 bits (15), Expect = 0.45
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 26  aataataataataat 40
           |||||||||||||||
Sbjct: 734 aataataataataat 748


 Score = 30.2 bits (15), Expect = 0.45
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 26  aataataataataat 40
           |||||||||||||||
Sbjct: 146 aataataataataat 160


 Score = 28.2 bits (14), Expect = 1.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 26  aataataataataa 39
           ||||||||||||||
Sbjct: 737 aataataataataa 750


 Score = 28.2 bits (14), Expect = 1.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 26  aataataataataa 39
           ||||||||||||||
Sbjct: 152 aataataataataa 165


 Score = 26.3 bits (13), Expect = 7.0
 Identities = 13/13 (100%)
 Strand = Plus / Plus

                        
Query: 28  taataataataat 40
           |||||||||||||
Sbjct: 145 taataataataat 157


  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: 17,734
Number of Sequences: 6905
Number of extensions: 17734
Number of successful extensions: 13448
Number of sequences better than 10.0: 2133
length of query: 115
length of database: 5,674,871
effective HSP length: 14
effective length of query: 101
effective length of database: 5,578,201
effective search space: 563398301
effective search space used: 563398301
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2008.12.22
Homology vs DNA 
Query= Contig-U14430-1 (Contig-U14430-1Q) /CSM_Contig/Contig-U14430-1Q.Seq.d
         (115 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

(BJ369515) Dictyostelium discoideum cDNA clone:ddc50h22, 5' ...   127   5e-32  2
(AJ400814) Dictyostelium discoideum srfA gene, alternative p...   127   2e-31  2
(CR847950) Zebrafish DNA sequence from clone DKEY-174P2 in l...    52   0.004  1
(AL591482) Zebrafish DNA sequence from clone BUSM1-116C14 in...    52   0.004  1
(AL591418) Zebrafish DNA sequence from clone BUSM1-139E19 in...    52   0.004  1
(AE014297) Drosophila melanogaster chromosome 3R, complete s...    52   0.004  1
(AC018479) Drosophila melanogaster, chromosome 3R, region 87...    52   0.004  1
(AC007752) Drosophila melanogaster, chromosome 3R, region 87...    52   0.004  1
(BX897715) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    52   0.004  1
(AC017336) Drosophila melanogaster, *** SEQUENCING IN PROGRE...    52   0.004  1
(AC094275) Rattus norvegicus clone CH230-3G17, *** SEQUENCIN...    40   0.010  2
(AC102970) Rattus norvegicus clone CH230-25L13, *** SEQUENCI...    40   0.010  2
(DH522199) Rattus norvegicus DNA, BAC clone: RNB1-020A07, 5'...    40   0.013  2
(AC008697) Homo sapiens chromosome 5 clone CTB-70D3, complet...    38   0.019  3
(AC096839) Rattus norvegicus clone CH230-1I18, *** SEQUENCIN...    36   0.034  2
(AE014175) Mus musculus piebald deletion region section 3 of...    38   0.036  2
(AC120617) Rattus norvegicus clone CH230-32I5, WORKING DRAFT...    38   0.036  2
(AC134104) Rattus norvegicus clone CH230-12I13, *** SEQUENCI...    38   0.036  2
(AC131551) Rattus norvegicus clone CH230-11A22, *** SEQUENCI...    36   0.036  2
(AC132556) Rattus norvegicus clone CH230-85H11, *** SEQUENCI...    38   0.036  2
(AC108263) Rattus norvegicus clone CH230-9N21, *** SEQUENCIN...    38   0.036  2
(AC127715) Rattus norvegicus clone CH230-59C22, *** SEQUENCI...    36   0.037  2
(AC127785) Rattus norvegicus clone CH230-127O17, *** SEQUENC...    36   0.037  2
(AC094826) Rattus norvegicus clone CH230-2O13, WORKING DRAFT...    38   0.037  2
(AC114118) Rattus norvegicus clone CH230-12I3, *** SEQUENCIN...    38   0.037  2
(AC120480) Rattus norvegicus clone CH230-28I10, *** SEQUENCI...    38   0.037  2
(AC116208) Rattus norvegicus clone CH230-129C14, WORKING DRA...    38   0.037  2
(AC095669) Rattus norvegicus clone CH230-8O18, WORKING DRAFT...    38   0.037  2
(AC098251) Rattus norvegicus clone CH230-1H23, *** SEQUENCIN...    38   0.037  2
(AC102815) Mus musculus chromosome 14, clone RP23-55A5, comp...    38   0.037  2
(AC051627) Genomic Sequence For Arabidopsis thaliana Clone T...    38   0.038  2
(CR063590) Forward strand read from insert in 3'HPRT inserti...    38   0.046  2
(BH267296) CH230-19C20.TJ CHORI-230 Segment 1 Rattus norvegi...    38   0.047  2
(CR403567) Arabidopsis thaliana T-DNA flanking sequence GK-8...    38   0.048  2
(CR403568) Arabidopsis thaliana T-DNA flanking sequence GK-8...    38   0.048  2
(AC008703) Homo sapiens chromosome 5 clone CTB-76P12, comple...    38   0.051  3
(CT033820) Zebrafish DNA sequence from clone CH211-197K14 in...    48   0.059  1
(AC073813) Mus musculus clone RP23-69B1, WORKING DRAFT SEQUE...    48   0.059  1
(ES765968) TFL_88_D08_E001.g1 USDA-Tifton Peanut Library TFL...    48   0.059  1
(AC078931) Mus musculus  BAC RP23-419E4 (Roswell Park Cancer...    32   0.075  5
(AC110136) Rattus norvegicus clone CH230-57B3, *** SEQUENCIN...    36   0.13   2
(AC127915) Rattus norvegicus clone CH230-236P17, *** SEQUENC...    36   0.13   2
(AC114456) Rattus norvegicus clone CH230-257D1, *** SEQUENCI...    36   0.13   2
(AC114201) Rattus norvegicus clone CH230-215N8, *** SEQUENCI...    36   0.13   2
(AC119784) Rattus norvegicus clone CH230-143A5, *** SEQUENCI...    36   0.14   2
(AC122188) Mus musculus BAC clone RP23-33B7 from chromosome ...    36   0.14   2
(AC140410) Mus musculus BAC clone RP23-141J11 from 10, compl...    36   0.14   2
(CU694816) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    40   0.14   3
(AC141953) Rattus norvegicus clone CH230-352F14, WORKING DRA...    36   0.14   2
(EX946017) lk49h05.g7 Gnetum female cone (NYBG) Gnetum gnemo...    36   0.18   2
(AZ369192) 1M0119H10R Mouse 10kb plasmid UUGC1M library Mus ...    36   0.18   2
(DH657831) Rattus norvegicus DNA, BAC clone: RNB1-203D12, 5'...    36   0.18   2
(DH652257) Rattus norvegicus DNA, BAC clone: RNB1-195K19, 5'...    36   0.18   2
(BU009497) QGJ10K05.yg.ab1 QG_EFGHJ lettuce serriola Lactuca...    38   0.19   2
(AL611092) Anopheles gambiae GSS SP6 end of clone 27O17 of l...    36   0.21   2
(CR318611) Zebrafish DNA sequence from clone DKEY-199F5 in l...    46   0.23   1
(AL954693) Zebrafish DNA sequence from clone BUSM1-146N9 in ...    46   0.23   1
(AL645571) Mouse DNA sequence from clone RP23-39H1 on chromo...    46   0.23   1
(AM477690) Vitis vinifera contig VV78X132645.4, whole genome...    46   0.23   1
(AC158306) Mus musculus chromosome 1 clone RP23-184G18 map 1...    46   0.23   1
(AC132563) Rattus norvegicus clone CH230-5C4, *** SEQUENCING...    46   0.23   1
(AC132157) Rattus norvegicus clone CH230-96C17, *** SEQUENCI...    46   0.23   1
(AC128514) Rattus norvegicus clone CH230-30K18, *** SEQUENCI...    46   0.23   1
(AC098095) Rattus norvegicus clone CH230-169F14, WORKING DRA...    46   0.23   1
(CU655973) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   0.23   1
(AC221433) Bos taurus clone CH240-407C15, WORKING DRAFT SEQU...    46   0.23   1
(AC219904) Bos taurus clone CH240-318M3, WORKING DRAFT SEQUE...    46   0.23   1
(AC192949) Pan troglodytes chromosome 12 clone CH251-578E8, ...    46   0.23   1
(AC165205) Callicebus moloch clone LB5-392D15, WORKING DRAFT...    46   0.23   1
(BH074410) RPCI-24-275L12.TJ RPCI-24 Mus musculus genomic cl...    46   0.23   1
(ET107366) QM0AAC14AG01RM1 CCH3 Citrus clementina genomic cl...    46   0.23   1
(CL555856) OB__Ba0006M02.f OB__Ba Oryza brachyantha genomic ...    46   0.23   1
(EB496196) 1099435200980 12-DrosW-norm-1P5Kb Drosophila will...    46   0.23   1
(EB487575) 1099341206969 12-DrosW-norm-1P5Kb Drosophila will...    46   0.23   1
(EB460135) 1099435227752 12-DrosW-std-1P6Kb Drosophila willi...    46   0.23   1
(CX291778) C04004G04SK FlavFr1 Citrus clementina cDNA clone ...    46   0.23   1
(CK937452) CGF1004780_E11 Developing fruit albedo at 80 DAFB...    46   0.23   1
(EY799644) CR05-C3-701-083-A08-CT.F Mandarin fruit, developm...    46   0.23   1
(EY664211) CS00-C1-101-064-B02-CT.F Sweet orange leaf, infec...    46   0.23   1
(EY663948) CS00-C1-101-061-B05-CT.F Sweet orange leaf, infec...    46   0.23   1
(EY662392) CS00-C1-101-043-F05-CT.F Sweet orange leaf, infec...    46   0.23   1
(AC123059) Mus musculus BAC clone RP23-188K16 from 15, compl...    40   0.24   2
(FK861638) 000004981973G14 D. serrata mRNA from different de...    32   0.27   3
(AC155313) Mus musculus BAC clone RP23-349D10 from chromosom...    40   0.27   2
(EA702412) Sequence 81291 from patent US 7365185.                  40   0.29   2
(EF974350) Mus musculus C57BL/6N IST12798G7HMF1 gene trap em...    40   0.32   2
(AC011842) Homo sapiens chromosome 8 clone RP11-289G21 map 8...    40   0.45   4
(AC105546) Rattus norvegicus clone CH230-199P7, WORKING DRAF...    32   0.48   2
(AC109682) Rattus norvegicus clone CH230-181O5, *** SEQUENCI...    32   0.48   2
(AC112730) Rattus norvegicus clone CH230-8B11, *** SEQUENCIN...    34   0.49   2
(AC094865) Rattus norvegicus clone CH230-6H1, WORKING DRAFT ...    34   0.49   2
(AC106130) Rattus norvegicus clone CH230-56B15, WORKING DRAF...    32   0.49   2
(AY657027) Mus musculus chromosome 6 clone GA_x54KRFPKN04:12...    34   0.49   2
(AC116069) Rattus norvegicus clone CH230-209F3, *** SEQUENCI...    32   0.49   2
(AC109931) Rattus norvegicus clone CH230-231J8, WORKING DRAF...    32   0.49   2
(AC130391) Rattus norvegicus clone CH230-4L5, WORKING DRAFT ...    34   0.50   2
(AC132796) Rattus norvegicus clone CH230-10M21, *** SEQUENCI...    32   0.50   2
(AC159715) Mus musculus 6 BAC RP23-367A13 (Roswell Park Canc...    34   0.50   2
(AC109756) Rattus norvegicus clone CH230-193G11, WORKING DRA...    32   0.50   2
(AC155332) Mus musculus 6 BAC RP24-140J8 (Roswell Park Cance...    34   0.50   2

>(BJ369515) Dictyostelium discoideum cDNA clone:ddc50h22, 5' end,
          single read.
          Length = 106

 Score =  127 bits (64), Expect(2) = 5e-32
 Identities = 64/64 (100%)
 Strand = Plus / Plus


Query: 1  ataccactttcaaacaaaaggaacaaataataataataattgtatcaataaccaatagaa 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  ataccactttcaaacaaaaggaacaaataataataataattgtatcaataaccaatagaa 60


Query: 61 ttaa 64
          ||||
Sbjct: 61 ttaa 64

 Score = 40.1 bits (20), Expect(2) = 5e-32
 Identities = 23/23 (100%)
 Strand = Plus / Plus


Query: 84  aaaaactttaacttttttnggaa 106
           |||||||||||||||||||||||
Sbjct: 84  aaaaactttaacttttttnggaa 106

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 132,618,366
Number of extensions: 15426006
Number of successful extensions: 7669974
Number of sequences better than 10.0: 853
Length of query: 115
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 93
Effective length of database: 93,199,600,587
Effective search space: 8667562854591
Effective search space used: 8667562854591
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7.11
Homology vs Protein 
Query= Contig-U14430-1 (Contig-U14430-1Q) /CSM_Contig/Contig-U14430-1Q.Seq.d
         (115 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: 50,670,307
Number of extensions: 1126872
Number of successful extensions: 1
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 0
Length of query: 38
Length of database: 1,051,180,864
Length adjustment: 12
Effective length of query: 26
Effective length of database: 1,012,342,156
Effective search space: 26320896056
Effective search space used: 26320896056
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: 24 (13.9 bits)
PSORT 

 psg: 0.98  gvh: 0.24  alm: 0.29  top: 0.53  tms: 0.07  mit: 0.33  mip: 0.00
 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: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 1.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 28.0 %: nuclear
	 20.0 %: mitochondrial
	 20.0 %: endoplasmic reticulum
	 16.0 %: cytoplasmic
	  8.0 %: plasma membrane
	  4.0 %: Golgi
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U14430-1 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