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-U12964-1
Contig ID Contig-U12964-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12964-1 (Contig-U12964-1Q) /CSM_Contig/Contig-U12964-1Q.Seq.d
AAATCAAACAATCAATTATAATCAAATAATTAAAAAATGTCTCTCTTTGC
TTCAATTTCATCAATCTCTAAAGTTAACTCAACCAAATCAACCTTGATTG
ATAATAAAAACTCAATGATCCAATTCACTGAAAATAAAGTCCAAACTGGT
TTAGTTAGTGGTTTATTGTTTAATGTTGCTGAGAGTTTAAATAAAGCTGG
TCTTTAAACTATTTAAAAAGTTTCTTTAATAAAGAAAAATAGTAATAATA
AAACTATAACAATAATTACAAAACAATAAAATTAACAATAAAATTTTAAA
ATAACAATAAATCAATAAATGGATATTTATTTTTAAATTTTATTGTTCCA
AAAAAAAAA
Gap no gap
Contig length 359
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 5699191
End point 5698832
Strand (PLUS/MINUS) MINUS
Number of clones 2
Number of EST 3
Link to clone list U12964
List of clone(s) 

est1=CHN613F,1,319
est2=CHN613Z,1,302
est3=CHF301F,6,360
Translated Amino Acid sequence 
ksnnql*snn*KMSLFASISSISKVNSTKSTLIDNKNSMIQFTENKVQTGLVSGLLFNVA
ESLNKAGL*ti*kvslikknsnnktitiitkq*n*q*nfkitinq*mdiyf*illfqkk
Translated Amino Acid sequence (All Frames) 
Frame A:
ksnnql*snn*KMSLFASISSISKVNSTKSTLIDNKNSMIQFTENKVQTGLVSGLLFNVA
ESLNKAGL*ti*kvslikknsnnktitiitkq*n*q*nfkitinq*mdiyf*illfqkk


Frame B:
nqtinynqiikkclsllqfhqslkltqpnqp*liiktq*snslkiksklv*lvvyclmll
rv*iklvfklfkkfl**rkiviikl*q*lqnnkinnkilk*q*inkwififkfycskkk


Frame C:
ikqsiiik*lknvslcfnfinl*s*lnqinld***klndpih*k*spnwfs*wfiv*cc*
efk*swslnylksffnkek****nynnnyktikltikf*nnnksingylflnfivpkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12964-1 (Contig-U12964-1Q)
/CSM_Contig/Contig-U12964-1Q.Seq.d
         (359 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12964-1 (Contig-U12964-1Q) /CSM_Contig/Conti...   446  e-126
Contig-U02001-1 (Contig-U02001-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U12705-1 (Contig-U12705-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U12221-1 (Contig-U12221-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U10359-1 (Contig-U10359-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U14719-1 (Contig-U14719-1Q) /CSM_Contig/Conti...    36  0.025
Contig-U13761-1 (Contig-U13761-1Q) /CSM_Contig/Conti...    36  0.025
Contig-U13067-1 (Contig-U13067-1Q) /CSM_Contig/Conti...    36  0.025
Contig-U05340-1 (Contig-U05340-1Q) /CSM_Contig/Conti...    36  0.025
Contig-U13857-1 (Contig-U13857-1Q) /CSM_Contig/Conti...    32  0.38

>Contig-U12964-1 (Contig-U12964-1Q) /CSM_Contig/Contig-U12964-1Q.Seq.d
          Length = 359

 Score =  446 bits (225), Expect = e-126
 Identities = 225/225 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aaatcaaacaatcaattataatcaaataattaaaaaatgtctctctttgcttcaatttca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaatcaaacaatcaattataatcaaataattaaaaaatgtctctctttgcttcaatttca 60

                                                                       
Query: 61  tcaatctctaaagttaactcaaccaaatcaaccttgattgataataaaaactcaatgatc 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tcaatctctaaagttaactcaaccaaatcaaccttgattgataataaaaactcaatgatc 120

                                                                       
Query: 121 caattcactgaaaataaagtccaaactggtttagttagtggtttattgtttaatgttgct 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 caattcactgaaaataaagtccaaactggtttagttagtggtttattgtttaatgttgct 180

                                                        
Query: 181 gagagtttaaataaagctggtctttaaactatttaaaaagtttct 225
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gagagtttaaataaagctggtctttaaactatttaaaaagtttct 225


 Score = 58.0 bits (29), Expect = 7e-09
 Identities = 29/29 (100%)
 Strand = Plus / Plus

                                        
Query: 321 ggatatttatttttaaattttattgttcc 349
           |||||||||||||||||||||||||||||
Sbjct: 321 ggatatttatttttaaattttattgttcc 349


 Score = 34.2 bits (17), Expect = 0.097
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                
Query: 327 ttatttttaaattttattgtt 347
           ||||||| |||||||||||||
Sbjct: 304 ttattttaaaattttattgtt 284


>Contig-U02001-1 (Contig-U02001-1Q) /CSM_Contig/Contig-U02001-1Q.Seq.d
          Length = 628

 Score = 40.1 bits (20), Expect = 0.002
 Identities = 23/24 (95%)
 Strand = Plus / Minus

                                   
Query: 65  tctctaaagttaactcaaccaaat 88
           ||||||||||||| ||||||||||
Sbjct: 199 tctctaaagttaattcaaccaaat 176


>Contig-U12705-1 (Contig-U12705-1Q) /CSM_Contig/Contig-U12705-1Q.Seq.d
          Length = 1157

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

                              
Query: 120 ccaattcactgaaaataaa 138
           |||||||||||||||||||
Sbjct: 249 ccaattcactgaaaataaa 267


  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: 8470
Number of Sequences: 6905
Number of extensions: 8470
Number of successful extensions: 1131
Number of sequences better than 10.0: 450
length of query: 359
length of database: 5,674,871
effective HSP length: 16
effective length of query: 343
effective length of database: 5,564,391
effective search space: 1908586113
effective search space used: 1908586113
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 2008.12. 4
Homology vs DNA 
Query= Contig-U12964-1 (Contig-U12964-1Q) /CSM_Contig/Contig-U12964-1Q.Seq.d
         (359 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

(BJ369047) Dictyostelium discoideum cDNA clone:ddc49i04, 5' ...   400   e-107  1
(BJ384341) Dictyostelium discoideum cDNA clone:ddc49i04, 3' ...   391   e-104  1
(BJ364509) Dictyostelium discoideum cDNA clone:ddc32b01, 5' ...   391   e-104  1
(AC010200) Homo sapiens 12 BAC RP11-575G13 (Roswell Park Can...    54   0.003  1
(AQ315722) RPCI11-98C7.TJ RPCI-11 Homo sapiens genomic clone...    54   0.003  1
(CL097638) ISB1-30B17_T7.1 ISB1 Xenopus (Silurana) tropicali...    50   0.054  1
(AC187604) Pan troglodytes BAC clone CH251-739K24 from chrom...    48   0.21   1
(AC123575) Medicago truncatula clone mth1-31p6, complete seq...    46   0.84   1
(AP009009) Bombyx mori genomic DNA, chromosome 4, BAC clone:...    46   0.84   1
(AC188209) Colobus guereza clone CH272-264F7, WORKING DRAFT ...    46   0.84   1
(AC188202) Papio hamadryas clone RP41-119B14, WORKING DRAFT ...    46   0.84   1
(DX932517) MUGQ_CH252P086J03T7_CP87_056 CHORI-252 Vervet Mon...    46   0.84   1
(DU682617) Bst015153 lambda03 Boechera stricta genomic clone...    46   0.84   1
(DU035744) 18107 Tomato HindIII BAC Library Solanum lycopers...    46   0.84   1
(DE552546) Bombyx mori genomic DNA, Fosmid clone:GBMFno189_a...    46   0.84   1
(DC200970) Plasmodium berghei cDNA clone:LV013799, liver sta...    46   0.84   1
(BF298017) 059PbC03 Pb cDNA #17, Tommaso Pace, Marta Ponzi, ...    46   0.84   1
(BF296011) 032PbG12 Pb cDNA #17, Tommaso Pace, Marta Ponzi, ...    46   0.84   1
(FD398265) 1106514257202 Cryptosporidium muris (strain RN66)...    46   0.84   1
(AM623405) Entamoeba invadens IP1 GSS, clone inv131d12.p1k.        42   1.0    2
(AI961215) wt15a09.x1 NCI_CGAP_Ut1 Homo sapiens cDNA clone I...    34   1.9    2
(ER495786) 1093015346876 Global-Ocean-Sampling_GS-35-01-01-1...    32   2.2    2
(BX548000) Zebrafish DNA sequence from clone CH211-199M8 in ...    38   3.1    2
(BC135170) Xenopus tropicalis hypothetical protein LOC100037...    44   3.3    1
(AC155981) Xenopus tropicalis clone CH216-71H15, complete se...    44   3.3    1
(AC151332) Xenopus tropicalis clone ISB-315C6, complete sequ...    44   3.3    1
(AC149872) Xenopus tropicalis clone CH216-115D10, complete s...    44   3.3    1
(AL805933) Mouse DNA sequence from clone RP23-31P9 on chromo...    44   3.3    1
(AL691503) Mouse DNA sequence from clone RP23-47N17 on chrom...    44   3.3    1
(AC122441) Mus musculus BAC clone RP24-225A21 from chromosom...    44   3.3    1
(CU468297) M.truncatula DNA sequence from clone MTH2-72A22 o...    44   3.3    1
(AM470929) Vitis vinifera, whole genome shotgun sequence, co...    44   3.3    1
(AC215630) Populus trichocarpa clone POP049-I09, complete se...    44   3.3    1
(AX345677) Sequence 748 from Patent WO0200928.                     44   3.3    1
(AP001528) Homo sapiens genomic DNA, chromosome 11q, clone:R...    44   3.3    1
(AC149519) Xenopus tropicalis clone CH216-82N11, WORKING DRA...    44   3.3    1
(AC132053) Rattus norvegicus clone CH230-90M14, *** SEQUENCI...    44   3.3    1
(CU856705) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.3    1
(CU467990) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.3    1
(CT797460) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.3    1
(AP003085) Homo sapiens genomic DNA, chromosome 11q clone:RP...    44   3.3    1
(AL954644) Mouse DNA sequence *** SEQUENCING CANCELLED *** f...    44   3.3    1
(AC221900) Bos taurus clone CH240-378I17, WORKING DRAFT SEQU...    44   3.3    1
(AC171461) Xenopus tropicalis clone CH216-8H16, WORKING DRAF...    44   3.3    1
(AC171459) Xenopus tropicalis clone CH216-7L20, WORKING DRAF...    44   3.3    1
(AC020673) Homo sapiens chromosome 11 clone RP11-437N4 map 1...    44   3.3    1
(AZ653417) 1M0527N03F Mouse 10kb plasmid UUGC1M library Mus ...    44   3.3    1
(EI479474) PV_GBa0091G22.f PV_GBa Phaseolus vulgaris genomic...    44   3.3    1
(EI437528) PV_GBa0031P09.f PV_GBa Phaseolus vulgaris genomic...    44   3.3    1
(CC584860) CH240_381B5.T7 CHORI-240 Bos taurus genomic clone...    44   3.3    1
(EL855307) CBXT12053.g1 NICHD_XGC_trop_25 Xenopus (Silurana)...    44   3.3    1
(EL855306) CBXT12053.b1 NICHD_XGC_trop_25 Xenopus (Silurana)...    44   3.3    1
(EL530429) EST_omor_eva_9582 omoreva mixed_tissue Osmerus mo...    44   3.3    1
(EL524563) EST_omor_eva_3716 omoreva mixed_tissue Osmerus mo...    44   3.3    1
(DC161579) Xenopus tropicalis NBRP cDNA clone:rst104d20, 3' ...    44   3.3    1
(DC143592) Xenopus tropicalis NBRP cDNA clone:rst36o10, 3' end.    44   3.3    1
(DC141996) Xenopus tropicalis NBRP cDNA clone:rst31c03, 3' end.    44   3.3    1
(DC140335) Xenopus tropicalis NBRP cDNA clone:rst25p08, 3' end.    44   3.3    1
(CX334398) JGI_XZT69902.rev NIH_XGC_tropTad5 Xenopus (Silura...    44   3.3    1
(CR449264) Xenopus tropicalis EST, clone TTbA050i16 3'.            44   3.3    1
(CR430711) Xenopus tropicalis EST, clone TTbA075h20 3'.            44   3.3    1
(CF343140) AGENCOURT_15223288 NICHD_XGC_Swb1 Xenopus (Silura...    44   3.3    1
(BX722668) Xenopus tropicalis EST, clone TTpA035h12 5'.            44   3.3    1
(BX695437) Xenopus tropicalis EST, clone TNeu080k17 3'.            44   3.3    1
(BF910336) CM4-UT0042-281000-386-e12 UT0042 Homo sapiens cDN...    44   3.3    1
(AC017763) Drosophila melanogaster, *** SEQUENCING IN PROGRE...    42   3.8    2
(EJ272923) 1095361000361 Global-Ocean-Sampling_GS-27-01-01-1...    38   4.1    2
(BX897728) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    30   5.8    2
(AM448157) Vitis vinifera, whole genome shotgun sequence, co...    38   5.9    3
(AL929075) Zebrafish DNA sequence from clone CH211-132B9 in ...    30   6.1    2
(BX005476) Zebrafish DNA sequence from clone CH211-124K10 in...    30   6.1    2
(AP010490) Lotus japonicus genomic DNA, chromosome 3, clone:...    38   7.3    3
(CU222524) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    38   8.0    4
(AC021523) Homo sapiens chromosome 8, clone RP11-336N16, com...    40   9.0    2
(DU264727) 1098574273143 CHORI-243 Ovis aries genomic clone ...    38   9.2    2
(BX469901) Zebrafish DNA sequence from clone CH211-150E8 in ...    40   9.9    4

>(BJ369047) Dictyostelium discoideum cDNA clone:ddc49i04, 5' end,
           single read.
          Length = 318

 Score =  400 bits (202), Expect = e-107
 Identities = 202/202 (100%)
 Strand = Plus / Plus


Query: 1   aaatcaaacaatcaattataatcaaataattaaaaaatgtctctctttgcttcaatttca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaatcaaacaatcaattataatcaaataattaaaaaatgtctctctttgcttcaatttca 60


Query: 61  tcaatctctaaagttaactcaaccaaatcaaccttgattgataataaaaactcaatgatc 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tcaatctctaaagttaactcaaccaaatcaaccttgattgataataaaaactcaatgatc 120


Query: 121 caattcactgaaaataaagtccaaactggtttagttagtggtttattgtttaatgttgct 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 caattcactgaaaataaagtccaaactggtttagttagtggtttattgtttaatgttgct 180


Query: 181 gagagtttaaataaagctggtc 202
           ||||||||||||||||||||||
Sbjct: 181 gagagtttaaataaagctggtc 202

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 306,703,671
Number of extensions: 19487233
Number of successful extensions: 1759277
Number of sequences better than 10.0: 77
Length of query: 359
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 336
Effective length of database: 93,106,754,628
Effective search space: 31283869555008
Effective search space used: 31283869555008
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 5
Homology vs Protein 
Query= Contig-U12964-1 (Contig-U12964-1Q) /CSM_Contig/Contig-U12964-1Q.Seq.d
         (359 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP001078_1637(CP001078|pid:none) Clostridium botulinum E3 str. A...    34   1.4
CR940347_912(CR940347|pid:none) Theileria annulata strain Ankara...    32   7.0
AY812601_1(AY812601|pid:none) Schistosoma japonicum SJCHGC07766 ...    32   9.2
AM292340_1(AM292340|pid:none) Tribolium castaneum gr19 gene for ...    32   9.2

>CP001078_1637(CP001078|pid:none) Clostridium botulinum E3 str.
           Alaska E43, complete genome.
          Length = 732

 Score = 34.3 bits (77), Expect = 1.4
 Identities = 16/49 (32%), Positives = 27/49 (55%)
 Frame = +1

Query: 58  SSISKVNSTKSTLIDNKNSMIQFTENKVQTGLVSGLLFNVAESLNKAGL 204
           SSISK+NS  ++L  N  + +Q   NK++  + +G +   A+    A L
Sbjct: 35  SSISKINSKSTSLAQNAGAQVQGVSNKIKAAIATGAVAIAAKKTGSAML 83

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: 390,429,944
Number of extensions: 6201122
Number of successful extensions: 17595
Number of sequences better than 10.0: 4
Number of HSP's gapped: 17584
Number of HSP's successfully gapped: 4
Length of query: 119
Length of database: 1,051,180,864
Length adjustment: 85
Effective length of query: 34
Effective length of database: 776,073,349
Effective search space: 26386493866
Effective search space used: 26386493866
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: 0.92  gvh: 0.55  alm: 0.43  top: 0.53  tms: 0.00  mit: 0.37  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 %: mitochondrial
	 24.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: extracellular, including cell wall
	  4.0 %: cytoskeletal
	  4.0 %: Golgi
	  4.0 %: endoplasmic reticulum
	  4.0 %: peroxisomal

>> prediction for Contig-U12964-1 is mit
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) 2
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0