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-U10646-1
Contig ID Contig-U10646-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U10646-1 (Contig-U10646-1Q) /CSM_Contig/Contig-U10646-1Q.Seq.d
ATTAATGCACATCACAAAAAAAGAAAAATTACTGTAATAATCTTATATTA
TCTTCAATAATATTATATTAAAAATAATTTGTATTCATAATTATTATTAT
TATTATTCAATACTATTTGAAATTTTATTAAAATTATTTTAATATAATTA
AAAAAAAAAAAAAAAAAAAAAAAAGATTTATATTTATTTTTCACTTGGGA
ATTGTTTTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 238
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 3404790
End point 3404552
Strand (PLUS/MINUS) MINUS
Number of clones 3
Number of EST 3
Link to clone list U10646
List of clone(s) 

est1=VFM612F,1,166
est2=VFL885F,43,159
est3=VSE244E,65,239
Translated Amino Acid sequence 
lmhitkkekll**SYIIFNNIILKIICIHNYYYYYSILFEILLKLF*yn*kkkkkkkkiy
iyfslgncfvkkkkkkkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
inahhkkrkitviilyylq*yyiknnlys*lllllfnti*nfikiili*lkkkkkkkkdl
ylfftwelfckkkkkkkkk


Frame B:
lmhitkkekll**SYIIFNNIILKIICIHNYYYYYSILFEILLKLF*yn*kkkkkkkkiy
iyfslgncfvkkkkkkkkk


Frame C:
*ctsqkkknycnnlilssiily*k*fvfiiiiiiiqyylkfy*nyfniikkkkkkkkrfi
fifhlgivl*kkkkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U10646-1 (Contig-U10646-1Q)
/CSM_Contig/Contig-U10646-1Q.Seq.d
         (238 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U10646-1 (Contig-U10646-1Q) /CSM_Contig/Conti...    72  3e-13
Contig-U00230-1 (Contig-U00230-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U14075-1 (Contig-U14075-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U10965-1 (Contig-U10965-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U10958-1 (Contig-U10958-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U10054-1 (Contig-U10054-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U09306-1 (Contig-U09306-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U04943-1 (Contig-U04943-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U04679-1 (Contig-U04679-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U04580-1 (Contig-U04580-1Q) /CSM_Contig/Conti...    32  0.25

>Contig-U10646-1 (Contig-U10646-1Q) /CSM_Contig/Contig-U10646-1Q.Seq.d
          Length = 238

 Score = 71.9 bits (36), Expect = 3e-13
 Identities = 36/36 (100%)
 Strand = Plus / Plus

                                               
Query: 175 gatttatatttatttttcacttgggaattgttttgt 210
           ||||||||||||||||||||||||||||||||||||
Sbjct: 175 gatttatatttatttttcacttgggaattgttttgt 210


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

                                         
Query: 29 ttactgtaataatcttatattatcttcaata 59
          |||||||||||||||||||||||||||||||
Sbjct: 29 ttactgtaataatcttatattatcttcaata 59


 Score = 30.2 bits (15), Expect = 0.99
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                         
Query: 1  attaatgcacatcac 15
          |||||||||||||||
Sbjct: 1  attaatgcacatcac 15


>Contig-U00230-1 (Contig-U00230-1Q) /CSM_Contig/Contig-U00230-1Q.Seq.d
          Length = 1754

 Score = 34.2 bits (17), Expect = 0.063
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 176 atttatatttatttttc 192
           |||||||||||||||||
Sbjct: 55  atttatatttatttttc 39


>Contig-U14075-1 (Contig-U14075-1Q) /CSM_Contig/Contig-U14075-1Q.Seq.d
          Length = 458

 Score = 32.2 bits (16), Expect = 0.25
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                          
Query: 35 taataatcttatatta 50
          ||||||||||||||||
Sbjct: 25 taataatcttatatta 10


  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: 2267
Number of Sequences: 6905
Number of extensions: 2267
Number of successful extensions: 695
Number of sequences better than 10.0: 107
length of query: 238
length of database: 5,674,871
effective HSP length: 15
effective length of query: 223
effective length of database: 5,571,296
effective search space: 1242399008
effective search space used: 1242399008
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 2008.11.21
Homology vs DNA 
Query= Contig-U10646-1 (Contig-U10646-1Q) /CSM_Contig/Contig-U10646-1Q.Seq.d
         (238 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

(M30467) D.discoideum uridine diphosphoglucose pyrophosphory...    72   8e-11  2
(AU262967) Dictyostelium discoideum vegetative cDNA clone:VS...    72   9e-09  1
(M27639) Dictyostelium discoideum UDP-glucose pyrophosphoryl...    48   0.14   1
(AC130613) Rattus norvegicus 1 BAC CH230-2P2 (Children's Hos...    44   2.1    1
(AC128039) Rattus norvegicus  BAC CH230-394A24 (Children's H...    44   2.1    1
(AC024852) Caenorhabditis elegans cosmid Y71F9AM, complete s...    44   2.1    1
(AC152645) Bos taurus clone CH240-16J22, WORKING DRAFT SEQUE...    44   2.1    1
(AC152627) Bos taurus clone CH240-6H4, WORKING DRAFT SEQUENC...    44   2.1    1
(AC163287) Mus musculus BAC clone RP23-279E21 from chromosom...    42   8.4    1
(AC121948) Mus musculus BAC clone RP24-215A14 from 8, comple...    42   8.4    1
(EU493683) Samoaia leonensis voucher 109375 NADH dehydrogena...    42   8.4    1
(AC155826) Mus musculus chromosome 8 clone RP23-12E20, WORKI...    42   8.4    1
(AC099141) Rattus norvegicus clone CH230-51N2, *** SEQUENCIN...    42   8.4    1
(AC073804) Mus musculus clone RP23-458N3, WORKING DRAFT SEQU...    42   8.4    1
(CT826385) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   8.4    1
(AC230855) Bos taurus clone CH240-497M12, WORKING DRAFT SEQU...    42   8.4    1
(AC191005) Zea mays chromosome 10 clone CH201-55K9; ZMMBBc00...    42   8.4    1
(AC172605) Bos taurus clone CH240-246K14, WORKING DRAFT SEQU...    42   8.4    1
(FH260673) CHO_OF4120xi03r1.ab1 CHO_OF4 Nicotiana tabacum ge...    42   8.4    1
(FH260599) CHO_OF4120xi03f1.ab1 CHO_OF4 Nicotiana tabacum ge...    42   8.4    1
(DU353289) 1098312004803 CHORI-243 Ovis aries genomic clone ...    42   8.4    1
(DU311797) 1098309464016 CHORI-243 Ovis aries genomic clone ...    42   8.4    1
(CZ924165) 1098421026987 CHORI-243 Ovis aries genomic clone ...    42   8.4    1
(CR014925) Reverse strand read from insert in 3'HPRT inserti...    42   8.4    1

>(M30467) D.discoideum uridine diphosphoglucose pyrophosphorylase
           (UDPGP1) gene, 5' end.
          Length = 1047

 Score = 71.9 bits (36), Expect(2) = 8e-11
 Identities = 36/36 (100%)
 Strand = Plus / Plus


Query: 175 gatttatatttatttttcacttgggaattgttttgt 210
           ||||||||||||||||||||||||||||||||||||
Sbjct: 336 gatttatatttatttttcacttgggaattgttttgt 371

 Score = 30.2 bits (15), Expect(2) = 8e-11
 Identities = 15/15 (100%)
 Strand = Plus / Plus


Query: 1   attaatgcacatcac 15
           |||||||||||||||
Sbjct: 165 attaatgcacatcac 179

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 86,474,722
Number of extensions: 7114448
Number of successful extensions: 1973696
Number of sequences better than 10.0: 24
Length of query: 238
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 215
Effective length of database: 93,106,754,628
Effective search space: 20017952245020
Effective search space used: 20017952245020
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.28
Homology vs Protein 
Query= Contig-U10646-1 (Contig-U10646-1Q) /CSM_Contig/Contig-U10646-1Q.Seq.d
         (238 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: 154,662,574
Number of extensions: 1320984
Number of successful extensions: 299
Number of sequences better than 10.0: 0
Number of HSP's gapped: 299
Number of HSP's successfully gapped: 0
Length of query: 79
Length of database: 1,040,966,779
Length adjustment: 50
Effective length of query: 29
Effective length of database: 880,752,529
Effective search space: 25541823341
Effective search space used: 25541823341
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: 27 (15.0 bits)
PSORT 

 psg: 0.83  gvh: 0.24  alm: 0.41  top: 0.53  tms: 0.00  mit: 0.31  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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
	 28.0 %: cytoplasmic
	 16.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: vacuolar
	  4.0 %: plasma membrane
	  4.0 %: extracellular, including cell wall

>> prediction for Contig-U10646-1 is nuc
VS (DIR, S) 1
VH (FL, L) 0
VF (FL, S) 2
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