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-U15416-1
Contig ID Contig-U15416-1
Contig update 2004. 6.11
Contig sequence 
>Contig-U15416-1 (Contig-U15416-1Q) /CSM_Contig/Contig-U15416-1Q.Seq.d
AAAAAAAAAAAAAAAAAAAAGATGGAGGATCGTTTACAAGAATTGAGAAA
TGCAGGTGGTGTTAAANCTGAAGTGGATAAAAAGAAAAAAGGTAAAAAGG
GAAAAGGAGGAGAAGAAACACCAGAGTCTCCATCAGAACCATCAGGATCA
AATTATGAAGATCCATCAATCAACGATATTGAATTAGGTCCAGATGATCC
AGAAGCATCTGAAGAATTTATGCCAGAATTTTATCAAGAAGTTGGTGTTT
TAAAAACTTTAATGACATCAGTTAAAAGGAGTGTAAGAAGTATAGAGGAC
AAATATGTTTTATCTTTAAATTCGATTAATGTTGATCAAGGTTCAAAATA
TGAAGATGATATACAACAAATGCTAGATGGTACAAATAAATCATTCTCTG
AATTA
Gap no gap
Contig length 405
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 2641310
End point 2640906
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U15416
List of clone(s) 

est1=SLC783F,1,405
Translated Amino Acid sequence 
KKKKKKKMEDRLQELRNAGGVKXEVDKKKKGKKGKGGEETPESPSEPSGSNYEDPSINDI
ELGPDDPEASEEFMPEFYQEVGVLKTLMTSVKRSVRSIEDKYVLSLNSINVDQGSKYEDD
IQQMLDGTNKSFSEL
Translated Amino Acid sequence (All Frames) 
Frame A:
KKKKKKKMEDRLQELRNAGGVKXEVDKKKKGKKGKGGEETPESPSEPSGSNYEDPSINDI
ELGPDDPEASEEFMPEFYQEVGVLKTLMTSVKRSVRSIEDKYVLSLNSINVDQGSKYEDD
IQQMLDGTNKSFSEL


Frame B:
kkkkkkrwrivykn*emqvvlxlkwikrkkvkrekeekkhqslhqnhqdqimkihqstil
n*vqmiqkhlknlcqnfikklvf*kl**hqlkgv*ev*rtnmfyl*irlmlikvqnmkmi
ynkc*mvqinhsln


Frame C:
kkkkkkdggsftriekcrwc*x*sg*kekr*kgkrrrrntrvsirtirikl*rsinqry*
irsr*srsi*riyarilsrswcfknfndis*keckkyrgqicfifkfd*c*srfki*r*y
ttnarwyk*iil*i
own update 2004. 6.23
Homology vs CSM-cDNA 
Query= Contig-U15416-1 (Contig-U15416-1Q)
/CSM_Contig/Contig-U15416-1Q.Seq.d
         (405 letters)

Database: CSM
           8402 sequences; 8,075,542 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U15416-1 (Contig-U15416-1Q) /CSM_Contig/Conti...   569  e-162
Contig-U11432-1 (Contig-U11432-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U11904-1 (Contig-U11904-1Q) /CSM_Contig/Conti...    36  0.040
Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U11405-1 (Contig-U11405-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U09745-1 (Contig-U09745-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U16271-1 (Contig-U16271-1Q) /CSM_Contig/Conti...    32  0.62
Contig-U15635-1 (Contig-U15635-1Q) /CSM_Contig/Conti...    32  0.62
Contig-U13986-1 (Contig-U13986-1Q) /CSM_Contig/Conti...    32  0.62
Contig-U12456-1 (Contig-U12456-1Q) /CSM_Contig/Conti...    32  0.62

>Contig-U15416-1 (Contig-U15416-1Q) /CSM_Contig/Contig-U15416-1Q.Seq.d
          Length = 405

 Score =  569 bits (287), Expect = e-162
 Identities = 287/287 (100%)
 Strand = Plus / Plus

                                                                       
Query: 119 caccagagtctccatcagaaccatcaggatcaaattatgaagatccatcaatcaacgata 178
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 119 caccagagtctccatcagaaccatcaggatcaaattatgaagatccatcaatcaacgata 178

                                                                       
Query: 179 ttgaattaggtccagatgatccagaagcatctgaagaatttatgccagaattttatcaag 238
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179 ttgaattaggtccagatgatccagaagcatctgaagaatttatgccagaattttatcaag 238

                                                                       
Query: 239 aagttggtgttttaaaaactttaatgacatcagttaaaaggagtgtaagaagtatagagg 298
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 239 aagttggtgttttaaaaactttaatgacatcagttaaaaggagtgtaagaagtatagagg 298

                                                                       
Query: 299 acaaatatgttttatctttaaattcgattaatgttgatcaaggttcaaaatatgaagatg 358
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 299 acaaatatgttttatctttaaattcgattaatgttgatcaaggttcaaaatatgaagatg 358

                                                          
Query: 359 atatacaacaaatgctagatggtacaaataaatcattctctgaatta 405
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 359 atatacaacaaatgctagatggtacaaataaatcattctctgaatta 405


 Score =  109 bits (55), Expect = 3e-24
 Identities = 58/58 (100%)
 Strand = Plus / Plus

                                                                    
Query: 21 gatggaggatcgtttacaagaattgagaaatgcaggtggtgttaaanctgaagtggat 78
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21 gatggaggatcgtttacaagaattgagaaatgcaggtggtgttaaanctgaagtggat 78


>Contig-U11432-1 (Contig-U11432-1Q) /CSM_Contig/Contig-U11432-1Q.Seq.d
          Length = 2068

 Score = 38.2 bits (19), Expect = 0.010
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                              
Query: 381 tacaaataaatcattctct 399
           |||||||||||||||||||
Sbjct: 671 tacaaataaatcattctct 653


>Contig-U11904-1 (Contig-U11904-1Q) /CSM_Contig/Contig-U11904-1Q.Seq.d
          Length = 1700

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

                             
Query: 246 tgttttaaaaactttaat 263
           ||||||||||||||||||
Sbjct: 295 tgttttaaaaactttaat 312


  Database: CSM
    Posted date:  Jun 21, 2004  1:35 PM
  Number of letters in database: 8,075,542
  Number of sequences in database:  8402
  
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: 5768
Number of Sequences: 8402
Number of extensions: 5768
Number of successful extensions: 589
Number of sequences better than 10.0: 165
length of query: 405
length of database: 8,075,542
effective HSP length: 16
effective length of query: 389
effective length of database: 7,941,110
effective search space: 3089091790
effective search space used: 3089091790
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. 1.25
Homology vs DNA 
Query= Contig-U15416-1 (Contig-U15416-1Q) /CSM_Contig/Contig-U15416-1Q.Seq.d
         (405 letters)

Database: ddbj_B
           98,226,423 sequences; 98,766,808,389 total letters

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

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

(AU061058) Dictyostelium discoideum slug cDNA, clone SLC783.      569   0.0    2
(AM423906) Vitis vinifera contig VV78X217621.5, whole genome...    46   0.99   1
(FI045285) CHO_OF6474xe12r1.ab1 CHO_OF6 Nicotiana tabacum ge...    46   0.99   1
(AL772340) Zebrafish DNA sequence from clone CH211-150G2 in ...    44   3.9    1
(BX247953) Mouse DNA sequence from clone RP23-289L21 on chro...    44   3.9    1
(DL003986) Surrogate Markers of Neuropathic Pain.                  44   3.9    1
(DD058273) HUMAN KINASES.                                          44   3.9    1
(CS246280) Sequence 219 from Patent WO2005119262.                  44   3.9    1
(CS246279) Sequence 218 from Patent WO2005119262.                  44   3.9    1
(CS246278) Sequence 217 from Patent WO2005119262.                  44   3.9    1
(CS165019) Sequence 1207 from Patent WO2005083125.                 44   3.9    1
(AX746180) Sequence 31 from Patent WO0208399.                      44   3.9    1
(AX166564) Sequence 55 from Patent WO0138503.                      44   3.9    1
(BC043292) Homo sapiens diacylglycerol kinase, eta, mRNA (cD...    44   3.9    1
(AL139328) Human DNA sequence from clone RP11-84N7 on chromo...    44   3.9    1
(AK302727) Homo sapiens cDNA FLJ61490 complete cds, highly s...    44   3.9    1
(AK302631) Homo sapiens cDNA FLJ57236 complete cds, highly s...    44   3.9    1
(AK289546) Homo sapiens cDNA FLJ77448 complete cds, highly s...    44   3.9    1
(AK122909) Homo sapiens cDNA FLJ16584 fis, clone TESTI400009...    44   3.9    1
(AC112510) Homo sapiens 3 BAC RP11-432A8 (Roswell Park Cance...    44   3.9    1
(AB078968) Homo sapiens DGKH-2 mRNA for diacylglycerol kinas...    44   3.9    1
(AB078967) Homo sapiens DGKH-1 mRNA for diacylglycerol kinas...    44   3.9    1
(AC107615) Homo sapiens chromosome 3 clone RP11-5L1, WORKING...    44   3.9    1
(CU694764) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.9    1
(CU571097) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.9    1
(AC021681) Homo sapiens clone RP11-5L1, WORKING DRAFT SEQUEN...    44   3.9    1
(BC044822) Homo sapiens cDNA clone IMAGE:4823178, containing...    44   3.9    1
(CT176660) Sus scrofa genomic clone CH242-17H12, genomic sur...    44   3.9    1
(BU101814) PRODG1GID589R1 Compugen_targeted_mRNA_sequencing ...    44   3.9    1
(BU101813) PRODG1GID589F1 Compugen_targeted_mRNA_sequencing ...    44   3.9    1
(BU101576) PRODG1GID103R1 Compugen_targeted_mRNA_sequencing ...    44   3.9    1
(BE087080) QV1-BT0679-020400-135-a04 BT0679 Homo sapiens cDN...    44   3.9    1
(FL789821) CCGF16139.g1 CCGF Panicum virgatum early floral b...    44   3.9    1
(CU928535) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    38   5.7    3
(CO179940) EC00574.3prime Exelixis FlyTag ML01 pSport-Tag21 ...    32   6.9    2

>(AU061058) Dictyostelium discoideum slug cDNA, clone SLC783.
          Length = 405

 Score =  569 bits (287), Expect(2) = 0.0
 Identities = 287/287 (100%)
 Strand = Plus / Plus


Query: 119 caccagagtctccatcagaaccatcaggatcaaattatgaagatccatcaatcaacgata 178
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 119 caccagagtctccatcagaaccatcaggatcaaattatgaagatccatcaatcaacgata 178


Query: 179 ttgaattaggtccagatgatccagaagcatctgaagaatttatgccagaattttatcaag 238
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179 ttgaattaggtccagatgatccagaagcatctgaagaatttatgccagaattttatcaag 238


Query: 239 aagttggtgttttaaaaactttaatgacatcagttaaaaggagtgtaagaagtatagagg 298
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 239 aagttggtgttttaaaaactttaatgacatcagttaaaaggagtgtaagaagtatagagg 298


Query: 299 acaaatatgttttatctttaaattcgattaatgttgatcaaggttcaaaatatgaagatg 358
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 299 acaaatatgttttatctttaaattcgattaatgttgatcaaggttcaaaatatgaagatg 358


Query: 359 atatacaacaaatgctagatggtacaaataaatcattctctgaatta 405
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 359 atatacaacaaatgctagatggtacaaataaatcattctctgaatta 405

 Score =  109 bits (55), Expect(2) = 0.0
 Identities = 58/58 (100%)
 Strand = Plus / Plus


Query: 21 gatggaggatcgtttacaagaattgagaaatgcaggtggtgttaaanctgaagtggat 78
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21 gatggaggatcgtttacaagaattgagaaatgcaggtggtgttaaanctgaagtggat 78

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 98226423
Number of Hits to DB: 427,416,822
Number of extensions: 24905281
Number of successful extensions: 1949414
Number of sequences better than 10.0: 35
Length of query: 405
Length of database: 98,766,808,389
Length adjustment: 23
Effective length of query: 382
Effective length of database: 96,507,600,660
Effective search space: 36865903452120
Effective search space used: 36865903452120
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.16
Homology vs Protein 
Query= Contig-U15416-1 (Contig-U15416-1Q) /CSM_Contig/Contig-U15416-1Q.Seq.d
         (405 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AL663021_4(AL663021|pid:none) Oryza sativa genomic DNA, chromoso...    35   0.83
CR855064_7(CR855064|pid:none) Oryza sativa genomic DNA, chromoso...    35   0.83
AM055943_195(AM055943|pid:none) Toxoplasma gondii RH, genomic DN...    35   1.1
CR382128_411(CR382128|pid:none) Yarrowia lipolytica strain CLIB1...    35   1.1
BC034871_1(BC034871|pid:none) Mus musculus multimerin 2, mRNA (c...    34   1.4
EU016652_35(EU016652|pid:none) Uncultured Group I marine crenarc...    34   1.4
FN357547_25(FN357547|pid:none) Schistosoma mansoni genome sequen...    34   1.8
EU016633_40(EU016633|pid:none) Uncultured Group I marine crenarc...    34   1.8
AF014122_1(AF014122|pid:none) Strongylocentrotus purpuratus synt...    33   3.1
BC068437_1(BC068437|pid:none) Danio rerio zgc:85979, mRNA (cDNA ...    33   3.1
AF333035_1(AF333035|pid:none) Strongylocentrotus purpuratus synt...    33   3.1
AP009240_1846(AP009240|pid:none) Escherichia coli SE11 DNA, comp...    33   4.1
(Q7XBW5) RecName: Full=Probable plastid-lipid-associated protein...    33   4.1
CP000269_2811(CP000269|pid:none) Janthinobacterium sp. Marseille...    33   4.1
AE005174_2676(AE005174|pid:none) Escherichia coli O157:H7 EDL933...    32   5.4
CU928145_2058(CU928145|pid:none) Escherichia coli 55989 chromoso...    32   5.4
AB426058_27(AB426058|pid:none) Escherichia coli O111:H- DNA, gen...    32   5.4
CP001164_2400(CP001164|pid:none) Escherichia coli O157:H7 str. E...    32   5.4
A90958(A90958) probable phage replication protein [imported] - E...    32   5.4
CP000847_218(CP000847|pid:none) Rickettsia akari str. Hartford, ...    32   7.0
BT031102_1(BT031102|pid:none) Drosophila melanogaster IP08063 fu...    32   7.0
(Q4L3I9) RecName: Full=Cysteinyl-tRNA synthetase;          EC=6....    32   9.2
AE016816_298(AE016816|pid:none) Ashbya gossypii (= Eremothecium ...    32   9.2
AM442013_1(AM442013|pid:none) Vitis vinifera contig VV78X248633....    32   9.2

>AL663021_4(AL663021|pid:none) Oryza sativa genomic DNA, chromosome 4,
            BAC clone: OSJNBa0041M06, complete sequence.
          Length = 2153

 Score = 35.0 bits (79), Expect = 0.83
 Identities = 19/56 (33%), Positives = 30/56 (53%)
 Frame = -3

Query: 403  IQRMIYLYHLAFVVYHLHILNLDQH*SNLKIKHICPLYFLHSF*LMSLKFLKHQLL 236
            +  ++ L HL   + H  +L L QH  +L+++H   L  LH   L+ L  L H+LL
Sbjct: 1623 VHHLLRLRHLLLRILHRLLLMLRQHRLHLRLQHRLLLRILHRLLLVLLHLLPHKLL 1678

Lambda     K      H
   0.305    0.127    0.341

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: 461,692,845
Number of extensions: 7387781
Number of successful extensions: 13656
Number of sequences better than 10.0: 24
Number of HSP's gapped: 13643
Number of HSP's successfully gapped: 24
Length of query: 135
Length of database: 1,051,180,864
Length adjustment: 99
Effective length of query: 36
Effective length of database: 730,761,523
Effective search space: 26307414828
Effective search space used: 26307414828
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.0 bits)
S2: 29 (15.8 bits)
PSORT 

 psg: 0.53  gvh: 0.29  alm: 0.54  top: 0.53  tms: 0.00  mit: 0.20  mip: 0.00
 nuc: 0.20  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 

	 68.0 %: nuclear
	 20.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U15416-1 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) 1
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