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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U14333-1
Contig ID Contig-U14333-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14333-1 (Contig-U14333-1Q) /CSM_Contig/Contig-U14333-1Q.Seq.d
NNNNNNNNNNAATTTCNATAAAATNTAATATTAGTAATATTACATGTGAT
GGATTTGATTAGGAATGTGAAATTCAGGGAAATAGTACCCNTTTTACAGT
TGATTATACAGCGGTTTATCATGTAAATTCAAATCCNATTTCNAAATATT
ATAATAGAAAGGTATGTATTAAATCAGTACCATATGGNACTTACTTATCA
AATAATAATGGTGTGATTGAAATGAGTGAAAAGCTACGTAAATATGAGGA
ATGGTTCATTGAAAGAGCTGCAACTGGTCCAAATTCATTGGATACTGATA
TCTATATTTTCAGGTAAAACATTCNACAAATATTTAACCTTTAATCCATC
AACGAATCAATTATTTCATGGTTCNATTTGTGAAAATAGTATATGGCGTT
TAGAAGGTAACNCTCAATTAAATCATGAAAAATTCN
Gap no gap
Contig length 436
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 5467303
End point 5467729
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U14333
List of clone(s) 

est1=CHH602Z,1,427
Translated Amino Acid sequence 
xxxisikxnisnitcdgfd*ECEIQGNSTXFTVDYTAVYHVNSNPISKYYNRKVCIKSVP
YGTYLSNNNGVIEMSEKLRKYEEWFIERAATGPNSLDTDIYIFR*nixqifnl*sinesi
iswfxl*k*ymafrr*xsiks*ki
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxfx*nxilvilhvmdlirnvkfreivpxlqliiqrfim*iqixfxniiieryvlnqy
hmxltyqiimv*lk*vksyvnmrngslkelqlvqihwilisifsgktfxkyltfnpstnq
lfhgsicensiwrlegnxqlnhekf


Frame B:
xxxnfxkx*y**yym*wi*lgm*nsgk*ypfys*lysglsckfksxfxil**kgmy*ist
iwxllik**wcd*ne*kat*i*gmvh*kscnwskfigy*ylyfqvkhstni*plihqrin
yfmvxfvkivygv*kvtln*imkns


Frame C:
xxxisikxnisnitcdgfd*ECEIQGNSTXFTVDYTAVYHVNSNPISKYYNRKVCIKSVP
YGTYLSNNNGVIEMSEKLRKYEEWFIERAATGPNSLDTDIYIFR*nixqifnl*sinesi
iswfxl*k*ymafrr*xsiks*ki
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14333-1 (Contig-U14333-1Q)
/CSM_Contig/Contig-U14333-1Q.Seq.d
         (436 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14333-1 (Contig-U14333-1Q) /CSM_Contig/Conti...   789  0.0
Contig-U09608-1 (Contig-U09608-1Q) /CSM_Contig/Conti...    38  0.008
Contig-U11185-1 (Contig-U11185-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U09464-1 (Contig-U09464-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U14532-1 (Contig-U14532-1Q) /CSM_Contig/Conti...    32  0.47
Contig-U14177-1 (Contig-U14177-1Q) /CSM_Contig/Conti...    32  0.47
Contig-U11642-1 (Contig-U11642-1Q) /CSM_Contig/Conti...    32  0.47
Contig-U09355-1 (Contig-U09355-1Q) /CSM_Contig/Conti...    32  0.47
Contig-U05090-1 (Contig-U05090-1Q) /CSM_Contig/Conti...    32  0.47

>Contig-U14333-1 (Contig-U14333-1Q) /CSM_Contig/Contig-U14333-1Q.Seq.d
          Length = 436

 Score =  789 bits (398), Expect = 0.0
 Identities = 425/425 (100%)
 Strand = Plus / Plus

                                                                       
Query: 11  aatttcnataaaatntaatattagtaatattacatgtgatggatttgattaggaatgtga 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11  aatttcnataaaatntaatattagtaatattacatgtgatggatttgattaggaatgtga 70

                                                                       
Query: 71  aattcagggaaatagtacccnttttacagttgattatacagcggtttatcatgtaaattc 130
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 71  aattcagggaaatagtacccnttttacagttgattatacagcggtttatcatgtaaattc 130

                                                                       
Query: 131 aaatccnatttcnaaatattataatagaaaggtatgtattaaatcagtaccatatggnac 190
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 131 aaatccnatttcnaaatattataatagaaaggtatgtattaaatcagtaccatatggnac 190

                                                                       
Query: 191 ttacttatcaaataataatggtgtgattgaaatgagtgaaaagctacgtaaatatgagga 250
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 191 ttacttatcaaataataatggtgtgattgaaatgagtgaaaagctacgtaaatatgagga 250

                                                                       
Query: 251 atggttcattgaaagagctgcaactggtccaaattcattggatactgatatctatatttt 310
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 251 atggttcattgaaagagctgcaactggtccaaattcattggatactgatatctatatttt 310

                                                                       
Query: 311 caggtaaaacattcnacaaatatttaacctttaatccatcaacgaatcaattatttcatg 370
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 311 caggtaaaacattcnacaaatatttaacctttaatccatcaacgaatcaattatttcatg 370

                                                                       
Query: 371 gttcnatttgtgaaaatagtatatggcgtttagaaggtaacnctcaattaaatcatgaaa 430
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 371 gttcnatttgtgaaaatagtatatggcgtttagaaggtaacnctcaattaaatcatgaaa 430

                
Query: 431 aattc 435
           |||||
Sbjct: 431 aattc 435


>Contig-U09608-1 (Contig-U09608-1Q) /CSM_Contig/Contig-U09608-1Q.Seq.d
          Length = 1109

 Score = 38.2 bits (19), Expect = 0.008
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                  
Query: 269 tgcaactggtccaaattcattgg 291
           |||||||||| ||||||||||||
Sbjct: 450 tgcaactggttcaaattcattgg 472


>Contig-U11185-1 (Contig-U11185-1Q) /CSM_Contig/Contig-U11185-1Q.Seq.d
          Length = 961

 Score = 34.2 bits (17), Expect = 0.12
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 198 tcaaataataatggtgt 214
           |||||||||||||||||
Sbjct: 462 tcaaataataatggtgt 478


  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: 4760
Number of Sequences: 6905
Number of extensions: 4760
Number of successful extensions: 504
Number of sequences better than 10.0: 127
length of query: 436
length of database: 5,674,871
effective HSP length: 16
effective length of query: 420
effective length of database: 5,564,391
effective search space: 2337044220
effective search space used: 2337044220
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 2008.12.21
Homology vs DNA 
Query= Contig-U14333-1 (Contig-U14333-1Q) /CSM_Contig/Contig-U14333-1Q.Seq.d
         (436 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

(BJ380099) Dictyostelium discoideum cDNA clone:ddc37c02, 3' ...   789   0.0    1
(BX470136) Zebrafish DNA sequence from clone CH211-113J6 in ...    48   0.26   1
(AL713869) Zebrafish DNA sequence from clone BUSM1-75P05 in ...    48   0.26   1
(CT963112) Medicago truncatula chromosome 5 clone mth2-117d2...    36   0.89   5
(BX649467) Zebrafish DNA sequence from clone CH211-117L16 in...    46   1.0    1
(CP000853) Alkaliphilus oremlandii OhILAs, complete genome.        46   1.0    1
(AC176903) Strongylocentrotus purpuratus clone R3-31O21, WOR...    40   1.2    3
(AC177489) Strongylocentrotus purpuratus clone R3-1030A24, W...    38   3.1    3
(AF422188) Acanthopagrus latus clone AL54 repeat region.           44   4.1    1
(AZ926662) 476.dis10a12.s1 Saccharomyces castellii NRRL Y-12...    44   4.1    1
(DE180659) Bombyx mori genomic DNA, Fosmid clone:RO0333-K20_R.     44   4.1    1
(BH956126) odg94f05.g1 B.oleracea002 Brassica oleracea genom...    44   4.1    1
(BX571731) Zebrafish DNA sequence from clone CH211-195D1 in ...    40   6.6    2
(AC179422) Strongylocentrotus purpuratus clone R3-62K1, WORK...    32   7.3    2
(AC179889) Strongylocentrotus purpuratus clone R3-1006E12, W...    32   7.5    2
(DV112622) CV03003B2A07.f1 CV03-normalized library Euphorbia...    38   8.6    2
(DV114901) CV03010A1H04.f1 CV03-normalized library Euphorbia...    38   9.0    2

>(BJ380099) Dictyostelium discoideum cDNA clone:ddc37c02, 3' end,
           single read.
          Length = 427

 Score =  789 bits (398), Expect = 0.0
 Identities = 425/425 (100%)
 Strand = Plus / Minus


Query: 11  aatttcnataaaatntaatattagtaatattacatgtgatggatttgattaggaatgtga 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 427 aatttcnataaaatntaatattagtaatattacatgtgatggatttgattaggaatgtga 368


Query: 71  aattcagggaaatagtacccnttttacagttgattatacagcggtttatcatgtaaattc 130
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 367 aattcagggaaatagtacccnttttacagttgattatacagcggtttatcatgtaaattc 308


Query: 131 aaatccnatttcnaaatattataatagaaaggtatgtattaaatcagtaccatatggnac 190
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 307 aaatccnatttcnaaatattataatagaaaggtatgtattaaatcagtaccatatggnac 248


Query: 191 ttacttatcaaataataatggtgtgattgaaatgagtgaaaagctacgtaaatatgagga 250
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247 ttacttatcaaataataatggtgtgattgaaatgagtgaaaagctacgtaaatatgagga 188


Query: 251 atggttcattgaaagagctgcaactggtccaaattcattggatactgatatctatatttt 310
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 187 atggttcattgaaagagctgcaactggtccaaattcattggatactgatatctatatttt 128


Query: 311 caggtaaaacattcnacaaatatttaacctttaatccatcaacgaatcaattatttcatg 370
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 127 caggtaaaacattcnacaaatatttaacctttaatccatcaacgaatcaattatttcatg 68


Query: 371 gttcnatttgtgaaaatagtatatggcgtttagaaggtaacnctcaattaaatcatgaaa 430
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67  gttcnatttgtgaaaatagtatatggcgtttagaaggtaacnctcaattaaatcatgaaa 8


Query: 431 aattc 435
           |||||
Sbjct: 7   aattc 3

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 423,519,921
Number of extensions: 23667450
Number of successful extensions: 1712289
Number of sequences better than 10.0: 17
Length of query: 436
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 413
Effective length of database: 93,106,754,628
Effective search space: 38453089661364
Effective search space used: 38453089661364
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.10
Homology vs Protein 
Query= Contig-U14333-1 (Contig-U14333-1Q) /CSM_Contig/Contig-U14333-1Q.Seq.d
         (436 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

EU176871_1(EU176871|pid:none) Pratylenchus coffeae GHF5 endogluc...    33   2.4
AJ965638_1(AJ965638|pid:none) Nyctotherus ovalis partial mRNA fo...    33   3.1
AJ965632_1(AJ965632|pid:none) Nyctotherus ovalis partial mRNA fo...    33   3.1
(Q12433) RecName: Full=Protein AHC1; AltName: Full=ADA HAT compl...    33   3.1
CP000029_1618(CP000029|pid:none) Staphylococcus epidermidis RP62...    32   5.3
AC116979_21(AC116979|pid:none) Dictyostelium discoideum chromoso...    32   9.1

>EU176871_1(EU176871|pid:none) Pratylenchus coffeae GHF5
           endoglucanase precursor (eng1) gene, complete cds.
          Length = 458

 Score = 33.5 bits (75), Expect = 2.4
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
 Frame = +3

Query: 72  IQGNSTXFTVDYTAVYHVNS--NPISKYYNRKVCIKSVPYGTYLSNNNGVIEMSEKLRKY 245
           + G++  +T+ Y A  H  S  +  +   N+KVC+    YGT  ++ NG ++ +
Sbjct: 206 VSGSNLCYTLHYYAATHKQSLRDKATAALNKKVCVFVTEYGTVSADGNGGVDSTSS---- 261

Query: 246 EEWF 257
           +EW+
Sbjct: 262 QEWW 265

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: 631,258,764
Number of extensions: 11554321
Number of successful extensions: 22250
Number of sequences better than 10.0: 6
Number of HSP's gapped: 22247
Number of HSP's successfully gapped: 6
Length of query: 145
Length of database: 1,051,180,864
Length adjustment: 108
Effective length of query: 37
Effective length of database: 701,632,492
Effective search space: 25960402204
Effective search space used: 25960402204
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: 0.75  gvh: 0.38  alm: 0.59  top: 0.53  tms: 0.00  mit: 0.08  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
	 24.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	 12.0 %: mitochondrial
	  4.0 %: Golgi
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U14333-1 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) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0