NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U07086-1
Contig ID Contig-U07086-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U07086-1 (Contig-U07086-1Q) /CSM_Contig/Contig-U07086-1Q.Seq.d
GCCATTGGTAATAATGCAGCTGTTGCACCAGCACCACCAAAAGATCCAGT
GGTGGTACCACATCAAAAAGGTAAGAGAGTCAATTATTACAAGAGAATTA
CAATCACTCCTCCTGGTCAACCAATGTCAATCATGGAGATGAAAGCTCTC
AAATATATCGAGACTAGAAGAAAAGCAATAGCATTTGCAAGAAAGAAGAA
CCAAGAATTGATCAATACACCATTCTTCACCAATATAACACAAGAGAATC
CAGGTAGATACAATGCATTCGGTATCAATGAATATCAACTCAGAAGATTG
GATTACTATTGGGAAGTACTTCAAAGAAATGGTCTATTCACTCATGAATC
TTTCCGTTATATTGCAAATGAATTGGGACTCAAATTTGAAACCATTCAAA
CCTGTCTCAAGAGTAGACGTGCAACTTATGCTGCTCATATCAACGAATTT
CGTATTAATCATAAACCAATCACTTTAATGAGAAAAGATCAATTGGTTCA
TGAAATTCAAAAAAGAGGTGGTATTGCTTATATCTGTATTCCAAAATATA
CACTTCTCGATAGATTAAGAGATCTTTTAAAAA
Gap no gap
Contig length 583
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 2376886
End point 2377472
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 2
Link to clone list U07086
List of clone(s) 

est1=VSK294Z,1,587
est2=VSK294F,2,488
Translated Amino Acid sequence 
AIGNNAAVAPAPPKDPVVVPHQKGKRVNYYKRITITPPGQPMSIMEMKALKYIETRRKAI
AFARKKNQELINTPFFTNITQENPGRYNAFGINEYQLRRLDYYWEVLQRNGLFTHESFRY
IANELGLKFETIQTCLKSRRATYAAHINEFRINHKPITLMRKDQLVHEIQKRGGIAYICI
PKYTLLDRLRDLLK
Translated Amino Acid sequence (All Frames) 
Frame A:
AIGNNAAVAPAPPKDPVVVPHQKGKRVNYYKRITITPPGQPMSIMEMKALKYIETRRKAI
AFARKKNQELINTPFFTNITQENPGRYNAFGINEYQLRRLDYYWEVLQRNGLFTHESFRY
IANELGLKFETIQTCLKSRRATYAAHINEFRINHKPITLMRKDQLVHEIQKRGGIAYICI
PKYTLLDRLRDLLK


Frame B:
plvimqllhqhhqkiqwwyhikkvresiitrelqslllvnqcqswr*klsnisrleekq*
hlqerrtkn*sihhsspi*hkriqvdtmhsvsmninsedwitigkyfkemvyslmnlsvi
lqmnwdsnlkpfkpvsrvdvqlmllistnfvliinqsl**ekinwfmkfkkevvllisvf
qnihfsid*eif*k


Frame C:
hw**cscctsttkrssggttskr*esqllqenynhsswstnvnhgdessqiyrd*kksns
ickkeepridqytilhqyntresr*iqciryq*istqkiglllgstskkwsihs*ifply
ck*igtqi*nhsnlsqe*tcnlccsyqrisy*s*tnhfnekrsigs*nskkrwyclylys
kiytsr*ikrsfk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U07086-1 (Contig-U07086-1Q)
/CSM_Contig/Contig-U07086-1Q.Seq.d
         (583 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U07086-1 (Contig-U07086-1Q) /CSM_Contig/Conti...  1156  0.0
Contig-U11252-1 (Contig-U11252-1Q) /CSM_Contig/Conti...    36  0.041
Contig-U10450-1 (Contig-U10450-1Q) /CSM_Contig/Conti...    36  0.041
Contig-U11920-1 (Contig-U11920-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U11367-1 (Contig-U11367-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U11216-1 (Contig-U11216-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U08388-1 (Contig-U08388-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U03180-1 (Contig-U03180-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U14027-1 (Contig-U14027-1Q) /CSM_Contig/Conti...    32  0.63

>Contig-U07086-1 (Contig-U07086-1Q) /CSM_Contig/Contig-U07086-1Q.Seq.d
          Length = 583

 Score = 1156 bits (583), Expect = 0.0
 Identities = 583/583 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   gccattggtaataatgcagctgttgcaccagcaccaccaaaagatccagtggtggtacca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gccattggtaataatgcagctgttgcaccagcaccaccaaaagatccagtggtggtacca 60

                                                                       
Query: 61  catcaaaaaggtaagagagtcaattattacaagagaattacaatcactcctcctggtcaa 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  catcaaaaaggtaagagagtcaattattacaagagaattacaatcactcctcctggtcaa 120

                                                                       
Query: 121 ccaatgtcaatcatggagatgaaagctctcaaatatatcgagactagaagaaaagcaata 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ccaatgtcaatcatggagatgaaagctctcaaatatatcgagactagaagaaaagcaata 180

                                                                       
Query: 181 gcatttgcaagaaagaagaaccaagaattgatcaatacaccattcttcaccaatataaca 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gcatttgcaagaaagaagaaccaagaattgatcaatacaccattcttcaccaatataaca 240

                                                                       
Query: 241 caagagaatccaggtagatacaatgcattcggtatcaatgaatatcaactcagaagattg 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 caagagaatccaggtagatacaatgcattcggtatcaatgaatatcaactcagaagattg 300

                                                                       
Query: 301 gattactattgggaagtacttcaaagaaatggtctattcactcatgaatctttccgttat 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 gattactattgggaagtacttcaaagaaatggtctattcactcatgaatctttccgttat 360

                                                                       
Query: 361 attgcaaatgaattgggactcaaatttgaaaccattcaaacctgtctcaagagtagacgt 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 attgcaaatgaattgggactcaaatttgaaaccattcaaacctgtctcaagagtagacgt 420

                                                                       
Query: 421 gcaacttatgctgctcatatcaacgaatttcgtattaatcataaaccaatcactttaatg 480
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 gcaacttatgctgctcatatcaacgaatttcgtattaatcataaaccaatcactttaatg 480

                                                                       
Query: 481 agaaaagatcaattggttcatgaaattcaaaaaagaggtggtattgcttatatctgtatt 540
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 agaaaagatcaattggttcatgaaattcaaaaaagaggtggtattgcttatatctgtatt 540

                                                      
Query: 541 ccaaaatatacacttctcgatagattaagagatcttttaaaaa 583
           |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 541 ccaaaatatacacttctcgatagattaagagatcttttaaaaa 583


>Contig-U11252-1 (Contig-U11252-1Q) /CSM_Contig/Contig-U11252-1Q.Seq.d
          Length = 1418

 Score = 36.2 bits (18), Expect = 0.041
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 183 atttgcaagaaagaagaa 200
           ||||||||||||||||||
Sbjct: 660 atttgcaagaaagaagaa 643


>Contig-U10450-1 (Contig-U10450-1Q) /CSM_Contig/Contig-U10450-1Q.Seq.d
          Length = 1082

 Score = 36.2 bits (18), Expect = 0.041
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                 
Query: 502 gaaattcaaaaaagaggtggta 523
           |||||| |||||||||||||||
Sbjct: 969 gaaattgaaaaaagaggtggta 990


  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: 5455
Number of Sequences: 6905
Number of extensions: 5455
Number of successful extensions: 494
Number of sequences better than 10.0: 151
length of query: 583
length of database: 5,674,871
effective HSP length: 16
effective length of query: 567
effective length of database: 5,564,391
effective search space: 3155009697
effective search space used: 3155009697
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 2008.11.11
Homology vs DNA 
Query= Contig-U07086-1 (Contig-U07086-1Q) /CSM_Contig/Contig-U07086-1Q.Seq.d
         (583 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

(AU270956) Dictyostelium discoideum vegetative cDNA clone:VS...  1156   0.0    1
(AU270955) Dictyostelium discoideum vegetative cDNA clone:VS...   959   0.0    1
(DU744490) ASNC2285.b2 HF10_10-07-02 uncultured marine micro...    48   0.35   1
(AC174821) Cavia porcellus clone CH234-215G14, WORKING DRAFT...    40   0.41   3
(AC111491) Rattus norvegicus clone CH230-111O19, *** SEQUENC...    46   1.4    1
(CU633224) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   1.4    1
(AP008006) Lotus japonicus genomic DNA, chromosome 3, clone:...    46   1.4    1
(AP007847) Lotus japonicus genomic DNA, chromosome 6, clone:...    46   1.4    1
(AC172052) Bos taurus clone CH240-282H8, WORKING DRAFT SEQUE...    46   1.4    1
(DE389621) Bombyx mori genomic DNA, BAC clone:11F10C.              46   1.4    1
(AC123849) Mus musculus BAC clone RP23-460B12 from chromosom...    44   1.8    2
(AC181231) Strongylocentrotus purpuratus clone R3-4010D12, W...    38   2.1    5
(FH941696) CHO_OF6729xd10f1.ab1 CHO_OF6 Nicotiana tabacum ge...    36   2.5    2
(FH143281) CHO_OF3723xb16r1.ab1 CHO_OF3 Nicotiana tabacum ge...    36   2.8    2
(BH334603) CH230-202L3.TJ CHORI-230 Segment 1 Rattus norvegi...    32   3.9    2
(AC015471) Homo sapiens chromosome 7 clone RP11-322G9 map 7,...    38   4.5    5
(CU856593) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.5    1
(CU606958) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.5    1
(AP003672) Mus musculus genomic DNA, chromosome 16q clone:RP...    44   5.5    1
(AP003658) Mus musculus genomic DNA, chromosome 16q clone:RP...    44   5.5    1
(EK266819) 1095462231110 Global-Ocean-Sampling_GS-31-01-01-1...    44   5.5    1
(DY272854) IC0AAA32BC06RM1 CitNFL Citrus clementina cDNA 5',...    44   5.5    1
(DY271159) KN0AAP9YA15FM1 Fruit-TF Citrus clementina cDNA 5'...    44   5.5    1
(DY259793) KN0AAP10YD11FM1 Fruit-TF Citrus clementina cDNA 5...    44   5.5    1
(CV710938) UCRPT01_0015C02_f Poncirus trifoliata CTV-challen...    44   5.5    1
(CO912539) USDA-FP_10633 Rough Lemon seedling root Citrus ja...    44   5.5    1
(AP001895) Homo sapiens genomic DNA, chromosome 18q12 clone:...    38   6.2    2
(AY696381) Borrelia burgdorferi strain 132b plasmid lp56 put...    30   8.4    3
(AY696392) Borrelia burgdorferi strain 132a plasmid lp56 put...    30   8.5    3
(AY696391) Borrelia burgdorferi strain 163b plasmid lp56 put...    30   8.5    3

>(AU270956) Dictyostelium discoideum vegetative cDNA clone:VSK294,
           3' end single read.
          Length = 587

 Score = 1156 bits (583), Expect = 0.0
 Identities = 583/583 (100%)
 Strand = Plus / Plus


Query: 1   gccattggtaataatgcagctgttgcaccagcaccaccaaaagatccagtggtggtacca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gccattggtaataatgcagctgttgcaccagcaccaccaaaagatccagtggtggtacca 60


Query: 61  catcaaaaaggtaagagagtcaattattacaagagaattacaatcactcctcctggtcaa 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  catcaaaaaggtaagagagtcaattattacaagagaattacaatcactcctcctggtcaa 120


Query: 121 ccaatgtcaatcatggagatgaaagctctcaaatatatcgagactagaagaaaagcaata 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ccaatgtcaatcatggagatgaaagctctcaaatatatcgagactagaagaaaagcaata 180


Query: 181 gcatttgcaagaaagaagaaccaagaattgatcaatacaccattcttcaccaatataaca 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gcatttgcaagaaagaagaaccaagaattgatcaatacaccattcttcaccaatataaca 240


Query: 241 caagagaatccaggtagatacaatgcattcggtatcaatgaatatcaactcagaagattg 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 caagagaatccaggtagatacaatgcattcggtatcaatgaatatcaactcagaagattg 300


Query: 301 gattactattgggaagtacttcaaagaaatggtctattcactcatgaatctttccgttat 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 gattactattgggaagtacttcaaagaaatggtctattcactcatgaatctttccgttat 360


Query: 361 attgcaaatgaattgggactcaaatttgaaaccattcaaacctgtctcaagagtagacgt 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 attgcaaatgaattgggactcaaatttgaaaccattcaaacctgtctcaagagtagacgt 420


Query: 421 gcaacttatgctgctcatatcaacgaatttcgtattaatcataaaccaatcactttaatg 480
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 gcaacttatgctgctcatatcaacgaatttcgtattaatcataaaccaatcactttaatg 480


Query: 481 agaaaagatcaattggttcatgaaattcaaaaaagaggtggtattgcttatatctgtatt 540
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 agaaaagatcaattggttcatgaaattcaaaaaagaggtggtattgcttatatctgtatt 540


Query: 541 ccaaaatatacacttctcgatagattaagagatcttttaaaaa 583
           |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 541 ccaaaatatacacttctcgatagattaagagatcttttaaaaa 583

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 670,656,153
Number of extensions: 38288768
Number of successful extensions: 2931628
Number of sequences better than 10.0: 31
Length of query: 583
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 560
Effective length of database: 93,106,754,628
Effective search space: 52139782591680
Effective search space used: 52139782591680
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 6.23
Homology vs Protein 
Query= Contig-U07086-1 (Contig-U07086-1Q) /CSM_Contig/Contig-U07086-1Q.Seq.d
         (583 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AL031744_3(AL031744|pid:none) Plasmodium falciparum DNA from MAL...    36   0.86
CP000439_1025(CP000439|pid:none) Francisella tularensis subsp. n...    34   2.5
AE017221_94(AE017221|pid:none) Thermus thermophilus HB27, comple...    34   3.3
AP008226_463(AP008226|pid:none) Thermus thermophilus HB8 genomic...    34   3.3
AK118732_1(AK118732|pid:none) Arabidopsis thaliana At3g30340 mRN...    33   4.3
CP000915_566(CP000915|pid:none) Francisella tularensis subsp. me...    33   5.6
AM233362_900(AM233362|pid:none) Francisella tularensis subsp. ho...    33   5.6
CP000608_893(CP000608|pid:none) Francisella tularensis subsp. tu...    33   5.6
CP000348_95(CP000348|pid:none) Leptospira borgpetersenii serovar...    33   7.3
CP000350_2589(CP000350|pid:none) Leptospira borgpetersenii serov...    33   7.3
AB208546_7(AB208546|pid:none) Echinococcus vogeli mitochondrial ...    32   9.5
AL662948_14(AL662948|pid:none) Oryza sativa genomic DNA, chromos...    32   9.5
EU392171_1(EU392171|pid:none) Hepatitis C virus isolate PB65185 ...    32   9.5

>AL031744_3(AL031744|pid:none) Plasmodium falciparum DNA from
           MAL1P1, complete sequence.
           &AL844501_128(AL844501|pid:none)
          Length = 2900

 Score = 35.8 bits (81), Expect = 0.86
 Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 1/100 (1%)
 Frame = +1

Query: 238 TQENPGRYNAFGINEYQLRRLDYY-WEVLQRNGLFTHESFRYIANELGLKFETIQTCLKS 414
           T+E  GR+N   IN   ++  +YY W  LQ+N L           E  LK+ + +
Sbjct: 116 TKEVEGRHNIIDIN--LIKNKNYYIWRELQKNVL-----------EYMLKYNSDKKNYFH 162

Query: 415 RRATYAAHINEFRINHKPITLMRKDQLVHEIQKRGGIAYI 534
               +   IN F  +   I +  KD+ + EI K+G + YI
Sbjct: 163 MSFEWNTIINSFLEDELKIKIKEKDRKIEEILKKGDLPYI 202

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: 939,655,695
Number of extensions: 19292723
Number of successful extensions: 55103
Number of sequences better than 10.0: 13
Number of HSP's gapped: 55079
Number of HSP's successfully gapped: 13
Length of query: 194
Length of database: 1,040,966,779
Length adjustment: 122
Effective length of query: 72
Effective length of database: 650,044,009
Effective search space: 46803168648
Effective search space used: 46803168648
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: 0.84  gvh: 0.32  alm: 0.50  top: 0.70  tms: 0.00  mit: 0.24  mip: 0.06
 nuc: 0.03  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: 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 

	 40.0 %: cytoplasmic
	 28.0 %: nuclear
	 12.0 %: cytoskeletal
	 12.0 %: mitochondrial
	  4.0 %: plasma membrane
	  4.0 %: peroxisomal

>> prediction for Contig-U07086-1 is cyt
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