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-U06832-1
Contig ID Contig-U06832-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06832-1 (Contig-U06832-1Q) /CSM_Contig/Contig-U06832-1Q.Seq.d
CAGCATTAAAAAAAACATTTAGACCATAGTGGTGAGTCTTAAAATCCCAA
CCAGTTAGTAGAGACTAAAAATCTACAAACAATAAACTCGATCTGATAAC
TGAAATGTCTTTTTTATTTTATTATTATTTTATTTAATTTTTTTATAATG
GTAATAGAAATGGAAATGATAATGTGACATCCTTGTTTACACCAACTAAA
ACTTTATTATATCTAAAGAAAACTAATTGCAATAAAAGAAGTTTAAGAAG
CAAAAAAAATAAAAATAAAAAAAAGTGATAATAATTTTATTGATGATAAT
AAATAATTATAAATTTGATCCTACAAAAAAAAA
Gap no gap
Contig length 333
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 961968
End point 962242
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 2
Link to clone list U06832
List of clone(s) 

est1=VSH113F,1,334
est2=VSH113Z,1,308
Translated Amino Acid sequence 
alkktfrp*w*vlksqpvsrd*kstnnkldlitemsflfyyyfi*FFYNGNRNGNDNVTS
LFTPTKTLLYLKKTNCNKRSLRSKKNKNKKK***fy****iiinlilqkk
Translated Amino Acid sequence (All Frames) 
Frame A:
qh*kkhldhsges*npnqlvetknlqtinsi**lkclfyfiiilfnffimviememim*h
pclhqlklyyi*rkliaikev*eakkikikksdnnfiddnk*l*i*sykkk


Frame B:
sikkni*tivvslkipts**rlkiykq*trsdn*nvffilllfylifl*w**kwk**cdi
lvytn*nfiisken*lq*kkfkkqkk*k*kkviiillmiinnykfdptkk


Frame C:
alkktfrp*w*vlksqpvsrd*kstnnkldlitemsflfyyyfi*FFYNGNRNGNDNVTS
LFTPTKTLLYLKKTNCNKRSLRSKKNKNKKK***fy****iiinlilqkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06832-1 (Contig-U06832-1Q)
/CSM_Contig/Contig-U06832-1Q.Seq.d
         (333 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06832-1 (Contig-U06832-1Q) /CSM_Contig/Conti...   208  3e-54
Contig-U06262-1 (Contig-U06262-1Q) /CSM_Contig/Conti...    92  4e-19
Contig-U12479-1 (Contig-U12479-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U14619-1 (Contig-U14619-1Q) /CSM_Contig/Conti...    36  0.023
Contig-U13187-1 (Contig-U13187-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U12208-1 (Contig-U12208-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U10938-1 (Contig-U10938-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U08709-1 (Contig-U08709-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U05223-1 (Contig-U05223-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U03313-1 (Contig-U03313-1Q) /CSM_Contig/Conti...    34  0.090

>Contig-U06832-1 (Contig-U06832-1Q) /CSM_Contig/Contig-U06832-1Q.Seq.d
          Length = 333

 Score =  208 bits (105), Expect = 3e-54
 Identities = 105/105 (100%)
 Strand = Plus / Plus

                                                                       
Query: 147 aatggtaatagaaatggaaatgataatgtgacatccttgtttacaccaactaaaacttta 206
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 147 aatggtaatagaaatggaaatgataatgtgacatccttgtttacaccaactaaaacttta 206

                                                        
Query: 207 ttatatctaaagaaaactaattgcaataaaagaagtttaagaagc 251
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 207 ttatatctaaagaaaactaattgcaataaaagaagtttaagaagc 251


 Score =  186 bits (94), Expect = 1e-47
 Identities = 94/94 (100%)
 Strand = Plus / Plus

                                                                       
Query: 16  catttagaccatagtggtgagtcttaaaatcccaaccagttagtagagactaaaaatcta 75
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16  catttagaccatagtggtgagtcttaaaatcccaaccagttagtagagactaaaaatcta 75

                                             
Query: 76  caaacaataaactcgatctgataactgaaatgtc 109
           ||||||||||||||||||||||||||||||||||
Sbjct: 76  caaacaataaactcgatctgataactgaaatgtc 109


 Score = 99.6 bits (50), Expect = 2e-21
 Identities = 50/50 (100%)
 Strand = Plus / Plus

                                                             
Query: 275 gtgataataattttattgatgataataaataattataaatttgatcctac 324
           ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 275 gtgataataattttattgatgataataaataattataaatttgatcctac 324


>Contig-U06262-1 (Contig-U06262-1Q) /CSM_Contig/Contig-U06262-1Q.Seq.d
          Length = 493

 Score = 91.7 bits (46), Expect = 4e-19
 Identities = 83/94 (88%), Gaps = 1/94 (1%)
 Strand = Plus / Plus

                                                                       
Query: 16  catttagaccatagtggtgagtcttaaaatcccaaccagttagtagagactaaaaatcta 75
           ||||||||| ||||| |||||||||||| ||| ||||||| ||||| | |||||||| ||
Sbjct: 16  catttagactatagttgtgagtcttaaattcc-aaccagtcagtagtggctaaaaattta 74

                                             
Query: 76  caaacaataaactcgatctgataactgaaatgtc 109
           ||||  || |||||||||||||||||||||||||
Sbjct: 75  caaaacatgaactcgatctgataactgaaatgtc 108


 Score = 34.2 bits (17), Expect = 0.090
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 230 caataaaagaagtttaa 246
           |||||||||||||||||
Sbjct: 223 caataaaagaagtttaa 239


>Contig-U12479-1 (Contig-U12479-1Q) /CSM_Contig/Contig-U12479-1Q.Seq.d
          Length = 1249

 Score = 38.2 bits (19), Expect = 0.006
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 191 accaactaaaactttatta 209
           |||||||||||||||||||
Sbjct: 679 accaactaaaactttatta 697


  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: 5616
Number of Sequences: 6905
Number of extensions: 5616
Number of successful extensions: 750
Number of sequences better than 10.0: 272
length of query: 333
length of database: 5,674,871
effective HSP length: 15
effective length of query: 318
effective length of database: 5,571,296
effective search space: 1771672128
effective search space used: 1771672128
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 2008.11.10
Homology vs DNA 
Query= Contig-U06832-1 (Contig-U06832-1Q) /CSM_Contig/Contig-U06832-1Q.Seq.d
         (333 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

(AU266929) Dictyostelium discoideum vegetative cDNA clone:VS...   206   e-123  3
(AU266930) Dictyostelium discoideum vegetative cDNA clone:VS...   208   1e-99  2
(EF551320) Dictyostelium discoideum non-coding RNA drf9-7, p...    58   1e-21  3
(AU261511) Dictyostelium discoideum vegetative cDNA clone:VS...    72   6e-18  3
(FE088438) LV_GL_RA36K17r Litopenaeus vannamei gills cDNA li...    44   0.004  2
(AC164475) Bos taurus clone CH240-149A14, *** SEQUENCING IN ...    44   0.14   3
(AC222622) Bos taurus clone CH240-444H3, WORKING DRAFT SEQUE...    42   0.19   2
(AM479789) Vitis vinifera contig VV79X001744.2, whole genome...    48   0.20   1
(AC187165) Glycine max clone gmw2-91b16, complete sequence.        48   0.20   1
(EY312266) CAWX23921.fwd CAWX Helobdella robusta Primary Ear...    48   0.20   1
(AC160169) Bos taurus clone CH240-83D1, WORKING DRAFT SEQUEN...    42   0.20   2
(AC174785) Bos taurus clone CH240-232O2, WORKING DRAFT SEQUE...    40   0.20   3
(AC163194) Bos taurus clone CH240-81E14, WORKING DRAFT SEQUE...    42   0.29   3
(AC172241) Bos taurus clone CH240-109C14, WORKING DRAFT SEQU...    42   0.42   3
(AC174203) Bos taurus clone CH240-310M23, WORKING DRAFT SEQU...    40   0.54   2
(ET757813) CHO_OF282xm08f2.ab1 CHO_OF Nicotiana tabacum geno...    34   0.61   2
(CU467677) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    40   0.65   2
(AC180006) Strongylocentrotus purpuratus clone R3-16N21, WOR...    42   0.68   2
(CU137720) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    38   0.68   3
(AC172247) Bos taurus clone CH240-159L15, WORKING DRAFT SEQU...    40   0.69   2
(BX470077) Zebrafish DNA sequence from clone CH211-136P17 in...    46   0.77   1
(AM411380) Oikopleura dioica if-C gene for intermediate fila...    46   0.77   1
(AE014841) Plasmodium falciparum 3D7 chromosome 11 section 6...    46   0.77   1
(AC155015) Bos taurus clone CH240-35H22, WORKING DRAFT SEQUE...    46   0.77   1
(AC110970) Rattus norvegicus clone CH230-302C22, *** SEQUENC...    46   0.77   1
(AC097187) Rattus norvegicus clone CH230-101L21, *** SEQUENC...    46   0.77   1
(AC230694) Bos taurus clone CH240-501P22, WORKING DRAFT SEQU...    46   0.77   1
(AC218350) Bos taurus clone CH240-286F18, WORKING DRAFT SEQU...    46   0.77   1
(AC164124) Bos taurus clone CH240-138E17, *** SEQUENCING IN ...    46   0.77   1
(EK127954) 1092994801064 Global-Ocean-Sampling_GS-31-01-01-1...    46   0.77   1
(EK108168) 1092963073568 Global-Ocean-Sampling_GS-31-01-01-1...    46   0.77   1
(EI412825) G05_hs5-25016312_PPan_040527.f Pan paniscus NG052...    46   0.77   1
(EG820722) EST_ssal_evd_22630 ssalevd thymus Salmo salar cDN...    46   0.77   1
(FH379635) CHO_OF4733xk24f1.ab1 CHO_OF4 Nicotiana tabacum ge...    34   0.79   2
(AC219237) Bos taurus clone CH240-333O10, WORKING DRAFT SEQU...    40   0.81   4
(FH681961) CHO_OF5064xc22r1.ab1 CHO_OF5 Nicotiana tabacum ge...    34   0.86   2
(FH044762) CHO_OF3193xo01r1.ab1 CHO_OF3 Nicotiana tabacum ge...    34   0.87   2
(FH543107) CHO_OF4762xg08r1.ab1 CHO_OF4 Nicotiana tabacum ge...    34   0.92   2
(AC182380) Bos taurus clone CH240-490G1, WORKING DRAFT SEQUE...    40   1.1    3
(AC223310) Bos taurus clone CH240-423B2, WORKING DRAFT SEQUE...    40   1.2    3
(AC183006) Bos taurus clone CH240-143N13, *** SEQUENCING IN ...    40   1.3    2
(AC185794) Bos taurus clone RP42-248J13, WORKING DRAFT SEQUE...    40   1.3    3
(AC182121) Bos taurus clone CH240-492O22, WORKING DRAFT SEQU...    40   1.4    3
(AM447718) Vitis vinifera, whole genome shotgun sequence, co...    34   1.8    2
(AC172641) Bos taurus clone CH240-265M2, WORKING DRAFT SEQUE...    40   2.1    2
(AC176691) Strongylocentrotus purpuratus clone R3-112B17, WO...    40   2.2    2
(AC160439) Bos taurus clone CH240-82B23, WORKING DRAFT SEQUE...    40   2.3    2
(CR335073) mte1-65H21RM1 BAC end, cultivar Jemalong A17 of M...    38   2.4    2
(AC172672) Bos taurus clone CH240-262J14, WORKING DRAFT SEQU...    40   2.4    2
(AC221658) Bos taurus clone CH240-389E14, WORKING DRAFT SEQU...    40   2.4    2
(CC514340) CH240_359K19.TARBAC13P2 CHORI-240 Bos taurus geno...    40   2.4    2
(AC230334) Bos taurus clone CH240-511N24, WORKING DRAFT SEQU...    40   2.4    2
(AC149699) Bos taurus clone CH240-401D1, WORKING DRAFT SEQUE...    38   2.5    2
(AC184428) Strongylocentrotus purpuratus clone R3-3076F14, W...    40   2.5    3
(AC163134) Bos taurus clone CH240-124I21, WORKING DRAFT SEQU...    38   2.5    2
(AC169812) Macaca mulatta clone CH250-89B10, WORKING DRAFT S...    38   2.6    2
(AC220565) Bos taurus clone CH240-352P15, WORKING DRAFT SEQU...    38   2.7    3
(AC013409) Homo sapiens BAC clone RP11-471D6 from 2, complet...    38   2.8    4
(AE014826) Plasmodium falciparum 3D7 chromosome 14 section 1...    40   2.8    5
(AC116957) Dictyostelium discoideum chromosome 2 map 1685067...    36   2.9    7
(AC178077) Strongylocentrotus purpuratus clone R3-3059N23, W...    38   2.9    3
(CU633743) Zebrafish DNA sequence from clone CH1073-303K20 i...    44   3.1    1
(CR382282) Zebrafish DNA sequence from clone CH211-208L4 in ...    44   3.1    1
(BX255913) Zebrafish DNA sequence from clone DKEY-85N7 in li...    44   3.1    1
(CR855082) Oryza sativa genomic DNA, chromosome 4, BAC clone...    44   3.1    1
(AP008210) Oryza sativa (japonica cultivar-group) genomic DN...    44   3.1    1
(AM465669) Vitis vinifera contig VV78X218424.7, whole genome...    44   3.1    1
(AM463280) Vitis vinifera contig VV78X023273.4, whole genome...    44   3.1    1
(AM444230) Vitis vinifera, whole genome shotgun sequence, co...    44   3.1    1
(AM425137) Vitis vinifera contig VV78X263213.7, whole genome...    44   3.1    1
(AL663022) Oryza sativa genomic DNA, chromosome 4, BAC clone...    44   3.1    1
(AL662986) Oryza sativa genomic DNA, chromosome 4, BAC clone...    44   3.1    1
(EA704052) Sequence 82931 from patent US 7365185.                  44   3.1    1
(EA704027) Sequence 82906 from patent US 7365185.                  44   3.1    1
(CS122302) Sequence 19 from Patent EP1550729.                      44   3.1    1
(AR063204) Sequence 8 from patent US 5844094.                      44   3.1    1
(AC016716) Homo sapiens BAC clone RP11-312I3 from 2, complet...    44   3.1    1
(AC161970) Bos taurus clone CH240-108K5, WORKING DRAFT SEQUE...    44   3.1    1
(AC159395) Bos taurus clone CH240-71M2, WORKING DRAFT SEQUEN...    44   3.1    1
(AC158817) Bos taurus clone CH240-64F11, WORKING DRAFT SEQUE...    44   3.1    1
(AC155029) Bos taurus clone CH240-32E12, WORKING DRAFT SEQUE...    44   3.1    1
(AC152319) Bos taurus clone CH240-2O16, WORKING DRAFT SEQUEN...    44   3.1    1
(AC150691) Bos taurus clone CH240-150E23, WORKING DRAFT SEQU...    44   3.1    1
(AC149672) Bos taurus clone CH240-55C19, WORKING DRAFT SEQUE...    44   3.1    1
(AC147391) Pan troglodytes chromosome UNK clone RP43-41M6, *...    44   3.1    1
(AC036217) Homo sapiens chromosome 2 clone RP11-678J16 map 2...    44   3.1    1
(CR385088) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    44   3.1    1
(CR383664) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    44   3.1    1
(AC230965) Bos taurus clone CH240-495A9, WORKING DRAFT SEQUE...    44   3.1    1
(AC230911) Bos taurus clone CH240-496C5, WORKING DRAFT SEQUE...    44   3.1    1
(AC222010) Bos taurus clone CH240-374J24, WORKING DRAFT SEQU...    44   3.1    1
(AC219826) Bos taurus clone CH240-320P15, WORKING DRAFT SEQU...    44   3.1    1
(AC187635) Pan troglodytes chromosome 7 clone CH251-279K8, W...    44   3.1    1
(AC171928) Bos taurus clone CH240-128G17, WORKING DRAFT SEQU...    44   3.1    1
(AC167486) Bos taurus clone CH240-194P13, WORKING DRAFT SEQU...    44   3.1    1
(AC165766) Bos taurus clone CH240-160G11, WORKING DRAFT SEQU...    44   3.1    1
(AC023348) Homo sapiens chromosome RPCI-11 clone RP11-543B23...    44   3.1    1
(EK009899) 1092955158019 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.1    1
(EJ638045) 1093006414578 Global-Ocean-Sampling_GS-29-01-01-1...    44   3.1    1
(EJ632425) 1092964806102 Global-Ocean-Sampling_GS-29-01-01-1...    44   3.1    1

>(AU266929) Dictyostelium discoideum vegetative cDNA clone:VSH113,
           5' end single read.
          Length = 333

 Score =  206 bits (104), Expect(3) = e-123
 Identities = 104/104 (100%)
 Strand = Plus / Plus


Query: 147 aatggtaatagaaatggaaatgataatgtgacatccttgtttacaccaactaaaacttta 206
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 147 aatggtaatagaaatggaaatgataatgtgacatccttgtttacaccaactaaaacttta 206


Query: 207 ttatatctaaagaaaactaattgcaataaaagaagtttaagaag 250
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 207 ttatatctaaagaaaactaattgcaataaaagaagtttaagaag 250

 Score =  186 bits (94), Expect(3) = e-123
 Identities = 94/94 (100%)
 Strand = Plus / Plus


Query: 16  catttagaccatagtggtgagtcttaaaatcccaaccagttagtagagactaaaaatcta 75
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16  catttagaccatagtggtgagtcttaaaatcccaaccagttagtagagactaaaaatcta 75


Query: 76  caaacaataaactcgatctgataactgaaatgtc 109
           ||||||||||||||||||||||||||||||||||
Sbjct: 76  caaacaataaactcgatctgataactgaaatgtc 109

 Score = 99.6 bits (50), Expect(3) = e-123
 Identities = 50/50 (100%)
 Strand = Plus / Plus


Query: 275 gtgataataattttattgatgataataaataattataaatttgatcctac 324
           ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 274 gtgataataattttattgatgataataaataattataaatttgatcctac 323

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 335,301,978
Number of extensions: 22718787
Number of successful extensions: 2001695
Number of sequences better than 10.0: 183
Length of query: 333
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 310
Effective length of database: 93,106,754,628
Effective search space: 28863093934680
Effective search space used: 28863093934680
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06832-1 (Contig-U06832-1Q) /CSM_Contig/Contig-U06832-1Q.Seq.d
         (333 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: 303,327,313
Number of extensions: 3456187
Number of successful extensions: 2544
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2544
Number of HSP's successfully gapped: 0
Length of query: 111
Length of database: 1,040,966,779
Length adjustment: 78
Effective length of query: 33
Effective length of database: 791,032,549
Effective search space: 26104074117
Effective search space used: 26104074117
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: 0.89  gvh: 0.33  alm: 0.57  top: 0.47  tms: 0.00  mit: 0.48  mip: 0.00
 nuc: 0.19  erl: 0.00  erm: 0.60  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 %: nuclear
	 32.0 %: mitochondrial
	 20.0 %: cytoplasmic

>> prediction for Contig-U06832-1 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