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-U01742-1
Contig ID Contig-U01742-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01742-1 (Contig-U01742-1Q) /CSM_Contig/Contig-U01742-1Q.Seq.d
TAAATTATTAAATATTCTTGTAGAAATAAAACTCCAATGATTAAAAGTTT
TATTTTTTATTTCATTTTTAATTTTTTTTTTATTTAAATAAATGTGTAGA
ATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAATTTTGATTAAATC
ATTTCCAAAATTAAAAAATATAGAATTTTATTTGTGTATATTTTTAATTG
TAGTATAAATTATAATCTAAATGATTAAATAAAGACGAAAAAAGTAAATC
ATTTTTATTTAACACCAAAAATTGTAATAAGCATTTTCATTTTTCAACAC
ACTCACACACTTTATAATCCACCAAATCATTTATTATTTTTTTATTTTTT
TATTCTTTAAAATCTAAAATAGATATTTTGGGTTTGTTTTTATGAATTTG
TTTTTATTATTGAA
Gap no gap
Contig length 414
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 4014954
End point 4014540
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U01742
List of clone(s) 

est1=SSG224Z,1,415
Translated Amino Acid sequence 
*iikyscrnktpmiksfifyfifnfffi*inv*n*kkkkkkkkkenfd*iiskikkyril
fvyifncsinynlnd*IKTKKVNHFYLTPKIVISIFIFQHTHTLYNPPNHLLFFYFFIL*
nlk*ifwvcfyefvfiie
Translated Amino Acid sequence (All Frames) 
Frame A:
*iikyscrnktpmiksfifyfifnfffi*inv*n*kkkkkkkkkenfd*iiskikkyril
fvyifncsinynlnd*IKTKKVNHFYLTPKIVISIFIFQHTHTLYNPPNHLLFFYFFIL*
nlk*ifwvcfyefvfiie


Frame B:
kllnilveiklq*lkvlffisflifflfk*mcrikkkkkkkkkkkiliksfpklkniefy
lciflivv*iii*mik*rrkk*iifi*hqkl**afsffntlthfiihqiiyyffiflffk
i*nryfgfvfmnlflll


Frame C:
ny*ifl*k*nsnd*kfyflfhf*fffylnkcvelkkkkkkkkkrkf*lnhfqn*ki*nfi
cvyf*l*ykl*sk*lnkdeksksflfntkncnkhfhfsthshtl*stksfiiflffyslk
skidilglfl*icfyy*
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01742-1 (Contig-U01742-1Q)
/CSM_Contig/Contig-U01742-1Q.Seq.d
         (414 letters)

Database: CSM
           8361 sequences; 7,895,291 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01742-1 (Contig-U01742-1Q) /CSM_Contig/Conti...   404  e-113
Contig-U11678-1 (Contig-U11678-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U13953-1 (Contig-U13953-1Q) /CSM_Contig/Conti...    36  0.040
Contig-U12242-1 (Contig-U12242-1Q) /CSM_Contig/Conti...    36  0.040
Contig-U05518-1 (Contig-U05518-1Q) /CSM_Contig/Conti...    36  0.040
Contig-U04642-1 (Contig-U04642-1Q) /CSM_Contig/Conti...    36  0.040
Contig-U04552-1 (Contig-U04552-1Q) /CSM_Contig/Conti...    36  0.040
Contig-U13464-1 (Contig-U13464-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U12500-1 (Contig-U12500-1Q) /CSM_Contig/Conti...    34  0.16

>Contig-U01742-1 (Contig-U01742-1Q) /CSM_Contig/Contig-U01742-1Q.Seq.d
          Length = 414

 Score =  404 bits (204), Expect = e-113
 Identities = 204/204 (100%)
 Strand = Plus / Plus

                                                                       
Query: 133 gaaaattttgattaaatcatttccaaaattaaaaaatatagaattttatttgtgtatatt 192
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 133 gaaaattttgattaaatcatttccaaaattaaaaaatatagaattttatttgtgtatatt 192

                                                                       
Query: 193 tttaattgtagtataaattataatctaaatgattaaataaagacgaaaaaagtaaatcat 252
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193 tttaattgtagtataaattataatctaaatgattaaataaagacgaaaaaagtaaatcat 252

                                                                       
Query: 253 ttttatttaacaccaaaaattgtaataagcattttcatttttcaacacactcacacactt 312
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 253 ttttatttaacaccaaaaattgtaataagcattttcatttttcaacacactcacacactt 312

                                   
Query: 313 tataatccaccaaatcatttatta 336
           ||||||||||||||||||||||||
Sbjct: 313 tataatccaccaaatcatttatta 336


 Score =  125 bits (63), Expect = 6e-29
 Identities = 63/63 (100%)
 Strand = Plus / Plus

                                                                       
Query: 352 attctttaaaatctaaaatagatattttgggtttgtttttatgaatttgtttttattatt 411
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 352 attctttaaaatctaaaatagatattttgggtttgtttttatgaatttgtttttattatt 411

              
Query: 412 gaa 414
           |||
Sbjct: 412 gaa 414


 Score = 93.7 bits (47), Expect = 2e-19
 Identities = 47/47 (100%)
 Strand = Plus / Plus

                                                         
Query: 1  taaattattaaatattcttgtagaaataaaactccaatgattaaaag 47
          |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  taaattattaaatattcttgtagaaataaaactccaatgattaaaag 47


 Score = 36.2 bits (18), Expect = 0.040
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 86  aaataaatgtgtagaatt 103
           ||||||||||||||||||
Sbjct: 86  aaataaatgtgtagaatt 103


>Contig-U11678-1 (Contig-U11678-1Q) /CSM_Contig/Contig-U11678-1Q.Seq.d
          Length = 1514

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 26/28 (92%)
 Strand = Plus / Minus

                                        
Query: 245  taaatcatttttatttaacaccaaaaat 272
            |||||| ||||||||||| |||||||||
Sbjct: 1062 taaatcttttttatttaataccaaaaat 1035


>Contig-U13953-1 (Contig-U13953-1Q) /CSM_Contig/Contig-U13953-1Q.Seq.d
          Length = 849

 Score = 36.2 bits (18), Expect = 0.040
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 161 ttaaaaaatatagaattt 178
           ||||||||||||||||||
Sbjct: 101 ttaaaaaatatagaattt 84


  Database: CSM
    Posted date:  Jun 7, 2004  8:33 AM
  Number of letters in database: 7,895,291
  Number of sequences in database:  8361
  
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: 17,373
Number of Sequences: 8361
Number of extensions: 17373
Number of successful extensions: 1702
Number of sequences better than 10.0: 583
length of query: 414
length of database: 7,895,291
effective HSP length: 16
effective length of query: 398
effective length of database: 7,761,515
effective search space: 3089082970
effective search space used: 3089082970
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. 5. 5
Homology vs DNA 
Query= Contig-U01742-1 (Contig-U01742-1Q) /CSM_Contig/Contig-U01742-1Q.Seq.d
         (414 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

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

(C89841) Dictyostelium discoideum slug cDNA, clone SSG224.        278   2e-95  3
(AC031976) Homo sapiens chromosome 18 clone RP11-288C17, WOR...    42   0.26   4
(AC119828) Mus musculus chromosome 10, clone RP23-186A24, co...    48   0.26   1
(EG344084) SAAH-aad30b03.g1 Agen 0058 Schmidtea mediterranea...    38   0.32   2
(AC094806) Rattus norvegicus clone CH230-5E5, WORKING DRAFT ...    36   0.56   2
(CR855864) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    40   0.96   2
(BX548248) Zebrafish DNA sequence from clone DKEY-245P14 in ...    46   1.0    1
(BX323590) Zebrafish DNA sequence from clone CH211-42I9 in l...    46   1.0    1
(BX072555) Zebrafish DNA sequence from clone DKEY-30O19 in l...    46   1.0    1
(BX001036) Zebrafish DNA sequence from clone CH211-155G22 in...    46   1.0    1
(AL845363) Zebrafish DNA sequence from clone CH211-14G12 in ...    46   1.0    1
(AC115584) Dictyostelium discoideum chromosome 2 map complem...    46   1.0    1
(AC156957) Bos taurus clone CH240-61C15, WORKING DRAFT SEQUE...    46   1.0    1
(CT990565) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    46   1.0    1
(BX470210) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    46   1.0    1
(AZ203369) SP_0077_B2_D07_T7A Strongylocentrotus purpuratus,...    46   1.0    1
(EJ484059) 1095403487264 Global-Ocean-Sampling_GS-28-01-01-1...    46   1.0    1
(BW636679) Dugesia ryukyuensis mRNA, clone: Dr_sW_006_D04, 5...    36   1.4    2
(AC117176) Dictyostelium discoideum chromosome 2 map 5018074...    40   1.8    4
(AX458634) Sequence 180 from Patent WO0246454.                     36   1.8    3
(BX649555) Zebrafish DNA sequence from clone CH211-117C13 in...    34   2.1    5
(CU694858) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    36   2.3    4
(AC110440) Rattus norvegicus clone CH230-310H6, WORKING DRAF...    38   3.7    2
(CR381592) Zebrafish DNA sequence from clone CH211-94B7 in l...    44   4.1    1
(AL357041) Human DNA sequence from clone RP11-221L2 on chrom...    44   4.1    1
(AC006500) Homo sapiens, clone hRPK.31_A_1, complete sequence.     44   4.1    1
(AC175886) Strongylocentrotus purpuratus clone R3-3043D21, W...    44   4.1    1
(FI100631) MUGQ_CH252P477P02T7_CH0157_001 CHORI-252 Vervet M...    44   4.1    1
(FH740151) CHO_OF5150xc08f1.ab1 CHO_OF5 Nicotiana tabacum ge...    44   4.1    1
(FH333173) CHO_OF4585xo22r1.ab1 CHO_OF4 Nicotiana tabacum ge...    44   4.1    1
(EJ772682) 1092973902986 Global-Ocean-Sampling_GS-30-02-01-1...    44   4.1    1
(AM605085) Entamoeba invadens IP1 GSS, clone inv044b02.q1k.        44   4.1    1
(AL737199) Danio rerio genomic clone DKEY-22M13, genomic sur...    44   4.1    1
(BI746884) rm33b06.y1 Meloidogyne arenaria egg pAMP1 v1 Chia...    44   4.1    1
(FF839155) EST_tthy_evl_881126 tthy_evl Thymallus thymallus ...    44   4.1    1
(AW688487) NF008B11ST1F1000 Developing stem Medicago truncat...    44   4.1    1
(ES577406) FPS015.CR_H16 LSG10-01 Lymnaea stagnalis cDNA clo...    44   4.1    1
(CT963106) Medicago truncatula chromosome 5 clone mth2-64o22...    36   4.5    5
(BX942812) Zebrafish DNA sequence from clone DKEY-7N6 in lin...    38   5.2    5
(EJ831390) 1093017582072 Global-Ocean-Sampling_GS-30-02-01-1...    38   5.4    2
(EJ912985) 1093018546868 Global-Ocean-Sampling_GS-30-02-01-1...    38   5.4    2
(EI471431) PV_GBa0079N23.r PV_GBa Phaseolus vulgaris genomic...    34   5.6    2
(EK315383) 1095462411185 Global-Ocean-Sampling_GS-31-01-01-1...    36   5.8    2
(EJ430933) 1093015255143 Global-Ocean-Sampling_GS-28-01-01-1...    36   6.4    2
(AC141471) Mus musculus BAC clone RP24-326K11 from 18, compl...    32   7.4    2
(AC132837) Mus musculus chromosome 18, clone RP24-490M12, co...    32   7.7    2
(AL772315) Mouse DNA sequence from clone RP23-54A13 on chrom...    40   8.0    3
(AM643554) Entamoeba dispar GSS, clone dispar87a06.p1k.            32   9.2    2

>(C89841) Dictyostelium discoideum slug cDNA, clone SSG224.
          Length = 415

 Score =  278 bits (140), Expect(3) = 2e-95
 Identities = 140/140 (100%)
 Strand = Plus / Plus


Query: 197 attgtagtataaattataatctaaatgattaaataaagacgaaaaaagtaaatcattttt 256
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 197 attgtagtataaattataatctaaatgattaaataaagacgaaaaaagtaaatcattttt 256


Query: 257 atttaacaccaaaaattgtaataagcattttcatttttcaacacactcacacactttata 316
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 257 atttaacaccaaaaattgtaataagcattttcatttttcaacacactcacacactttata 316


Query: 317 atccaccaaatcatttatta 336
           ||||||||||||||||||||
Sbjct: 317 atccaccaaatcatttatta 336

 Score = 93.7 bits (47), Expect(3) = 2e-95
 Identities = 47/47 (100%)
 Strand = Plus / Plus


Query: 1  taaattattaaatattcttgtagaaataaaactccaatgattaaaag 47
          |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  taaattattaaatattcttgtagaaataaaactccaatgattaaaag 47

 Score = 36.2 bits (18), Expect(3) = 2e-95
 Identities = 18/18 (100%)
 Strand = Plus / Plus


Query: 86  aaataaatgtgtagaatt 103
           ||||||||||||||||||
Sbjct: 86  aaataaatgtgtagaatt 103

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 355,142,472
Number of extensions: 24996434
Number of successful extensions: 2313859
Number of sequences better than 10.0: 49
Length of query: 414
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 391
Effective length of database: 99,442,330,388
Effective search space: 38881951181708
Effective search space used: 38881951181708
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01742-1 (Contig-U01742-1Q) /CSM_Contig/Contig-U01742-1Q.Seq.d
         (414 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

EU124719_11(EU124719|pid:none) Friesea grisea mitochondrion, com...    33   3.1

>EU124719_11(EU124719|pid:none) Friesea grisea mitochondrion,
           complete genome.
          Length = 166

 Score = 33.1 bits (74), Expect = 3.1
 Identities = 20/40 (50%), Positives = 24/40 (60%)
 Frame = +1

Query: 175 ILFVYIFNCSINYNLND*IKTKKVNHFYLTPKIVISIFIF 294
           ILF+YI + + N NL     T   N F LT  I+ISIFIF
Sbjct: 63  ILFIYIVSLASNSNL-----TISHNKFLLTSLIIISIFIF 97

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: 415,226,526
Number of extensions: 5721768
Number of successful extensions: 12128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 12125
Number of HSP's successfully gapped: 1
Length of query: 138
Length of database: 1,051,180,864
Length adjustment: 102
Effective length of query: 36
Effective length of database: 721,051,846
Effective search space: 25957866456
Effective search space used: 25957866456
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: 29 (15.8 bits)
PSORT 

 psg: 0.77  gvh: 0.50  alm: 0.39  top: 0.53  tms: 0.00  mit: 0.41  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: 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 %: nuclear
	 36.0 %: mitochondrial
	 20.0 %: cytoplasmic
	  4.0 %: cytoskeletal

>> prediction for Contig-U01742-1 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) 1
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