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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-U13718-1
Contig ID Contig-U13718-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13718-1 (Contig-U13718-1Q) /CSM_Contig/Contig-U13718-1Q.Seq.d
TTATTTTATTTTTTTATATTCTTTTTTTTTTTTTAAAAATATATATTACA
ATTNATTTATTTATTAAACNAATATATTTTNTTAGTATNCAAAAAANCAA
TCAATTAATAGTNCTATTACTTNAATTTTNGNNNNNNNNN
Gap no gap
Contig length 140
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U13718
List of clone(s) 

est1=VHK495F,1,131
Translated Amino Acid sequence 
ILFFYILFFFLKIYITIXLFIKXIYFXSXQKXNQLIVLLLXFXXXX
Translated Amino Acid sequence (All Frames) 
Frame A:
lfyffifffff*kyilqxiyllnxyixlvxkkxin**xyyxnfxxx


Frame B:
yfiflysffffkniyynxfiy*tnifx*yxkxqsinsxitxixxxx


Frame C:
ILFFYILFFFLKIYITIXLFIKXIYFXSXQKXNQLIVLLLXFXXXX
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13718-1 (Contig-U13718-1Q)
/CSM_Contig/Contig-U13718-1Q.Seq.d
         (140 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13718-1 (Contig-U13718-1Q) /CSM_Contig/Conti...   111  2e-25
Contig-U11344-1 (Contig-U11344-1Q) /CSM_Contig/Conti...   111  2e-25
Contig-U05223-1 (Contig-U05223-1Q) /CSM_Contig/Conti...    36  0.009
Contig-U14426-1 (Contig-U14426-1Q) /CSM_Contig/Conti...    34  0.035
Contig-U09946-1 (Contig-U09946-1Q) /CSM_Contig/Conti...    34  0.035
Contig-U08199-1 (Contig-U08199-1Q) /CSM_Contig/Conti...    34  0.035
Contig-U06990-1 (Contig-U06990-1Q) /CSM_Contig/Conti...    32  0.14
Contig-U06737-1 (Contig-U06737-1Q) /CSM_Contig/Conti...    32  0.14
Contig-U05634-1 (Contig-U05634-1Q) /CSM_Contig/Conti...    32  0.14
Contig-U14248-1 (Contig-U14248-1Q) /CSM_Contig/Conti...    30  0.55

>Contig-U13718-1 (Contig-U13718-1Q) /CSM_Contig/Contig-U13718-1Q.Seq.d
          Length = 140

 Score =  111 bits (56), Expect = 2e-25
 Identities = 89/95 (93%)
 Strand = Plus / Plus

                                                                       
Query: 35  aaaaatatatattacaattnatttatttattaaacnaatatannnnnnnagtatncaaaa 94
           ||||||||||||||||||||||||||||||||||||||||||    |  |||||||||||
Sbjct: 35  aaaaatatatattacaattnatttatttattaaacnaatatattttnttagtatncaaaa 94

                                              
Query: 95  aancaatcaattaatagtnctattacttnaatttt 129
           |||||||||||||||||||||||||||||||||||
Sbjct: 95  aancaatcaattaatagtnctattacttnaatttt 129


>Contig-U11344-1 (Contig-U11344-1Q) /CSM_Contig/Contig-U11344-1Q.Seq.d
          Length = 1802

 Score =  111 bits (56), Expect = 2e-25
 Identities = 82/95 (86%)
 Strand = Plus / Plus

                                                                       
Query: 35  aaaaatatatattacaattnatttatttattaaacnaatatannnnnnnagtatncaaaa 94
           ||||||||||||||||||| ||||||||||||||| ||||||       ||||| |||||
Sbjct: 3   aaaaatatatattacaatttatttatttattaaacgaatatattttcttagtatacaaaa 62

                                              
Query: 95  aancaatcaattaatagtnctattacttnaatttt 129
           || ||||||||||||||| ||||||||| ||||||
Sbjct: 63  aaacaatcaattaatagtactattactttaatttt 97


>Contig-U05223-1 (Contig-U05223-1Q) /CSM_Contig/Contig-U05223-1Q.Seq.d
          Length = 863

 Score = 36.2 bits (18), Expect = 0.009
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                
Query: 45  attacaattnatttatttatt 65
           ||||||||| |||||||||||
Sbjct: 834 attacaatttatttatttatt 814


  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: 3772
Number of Sequences: 6905
Number of extensions: 3772
Number of successful extensions: 1921
Number of sequences better than 10.0: 340
length of query: 140
length of database: 5,674,871
effective HSP length: 15
effective length of query: 125
effective length of database: 5,571,296
effective search space: 696412000
effective search space used: 696412000
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2008.12.13
Homology vs DNA 
Query= Contig-U13718-1 (Contig-U13718-1Q) /CSM_Contig/Contig-U13718-1Q.Seq.d
         (140 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

(AY047364) Dictyostelium discoideum cAMP phosphodiesterase (...   147   1e-31  1
(AC116979) Dictyostelium discoideum chromosome 2 map 6445720...   147   1e-31  1
(BJ426808) Dictyostelium discoideum cDNA clone:ddv60g08, 5' ...   147   1e-31  1
(BJ424279) Dictyostelium discoideum cDNA clone:ddv51n24, 5' ...   147   1e-31  1
(BJ418140) Dictyostelium discoideum cDNA clone:ddv31e20, 5' ...   147   1e-31  1
(BJ338082) Dictyostelium discoideum cDNA clone:dda60d04, 5' ...   147   1e-31  1
(BJ336011) Dictyostelium discoideum cDNA clone:dda52l09, 5' ...   147   1e-31  1
(BJ335781) Dictyostelium discoideum cDNA clone:dda51d16, 5' ...   147   1e-31  1
(BJ368690) Dictyostelium discoideum cDNA clone:ddc47p15, 5' ...   131   6e-27  1
(BJ418761) Dictyostelium discoideum cDNA clone:ddv33l22, 5' ...   127   1e-25  1
(BJ333504) Dictyostelium discoideum cDNA clone:dda43a02, 5' ...   117   1e-22  1
(BJ367383) Dictyostelium discoideum cDNA clone:ddc42c16, 5' ...   113   2e-21  1
(AE014817) Plasmodium falciparum 3D7 chromosome 14 section 2...    38   0.046  2
(FH744630) CHO_OF5175xd01r1.ab1 CHO_OF5 Nicotiana tabacum ge...    46   0.29   1
(FH047852) CHO_OF3305xo04f1.ab1 CHO_OF3 Nicotiana tabacum ge...    46   0.29   1
(ED402756) AUAC-aae49f11.g1 Ascaris suum whole genome shotgu...    46   0.29   1
(ED347166) AUAC-aaz13a08.g1 Ascaris suum whole genome shotgu...    46   0.29   1
(ED196256) AUAC-aax84c05.b1 Ascaris suum whole genome shotgu...    46   0.29   1
(ED044132) AUAC-aac11h11.g1 Ascaris suum whole genome shotgu...    46   0.29   1
(BX957246) Zebrafish DNA sequence from clone CH211-89F7 in l...    44   1.2    1
(AL808142) Mouse DNA sequence from clone RP23-84B8 on chromo...    44   1.2    1
(AL136998) Mouse DNA sequence from clone RP21-509E24 on chro...    44   1.2    1
(AC099796) Homo sapiens chromosome 1 clone RP5-866L20, compl...    44   1.2    1
(AC011736) Homo sapiens BAC clone CTD-2331A14 from 1, comple...    44   1.2    1
(AC036239) Homo sapiens chromosome 3 clone RP11-313K17, WORK...    44   1.2    1
(CW502314) fsbb001f298j10k0 Sorghum methylation filtered lib...    44   1.2    1
(CW420597) fsbb001f126p22f0 Sorghum methylation filtered lib...    44   1.2    1
(CW335743) 104_834_11483205_116_36082_083 Sorghum methylatio...    44   1.2    1
(CW335080) 104_833_11482846_116_36077_083 Sorghum methylatio...    44   1.2    1
(CW112498) 104_486_11104919_148_34541_090 Sorghum methylatio...    44   1.2    1
(CL195895) 104_421_10942693_114_32310_053 Sorghum methylatio...    44   1.2    1
(BZ368328) id12f12.b1 WGS-SbicolorF (JM107 adapted methyl fi...    44   1.2    1
(BX004823) Zebrafish DNA sequence from clone DKEY-13A3 in li...    34   2.3    2
(CR626869) Zebrafish DNA sequence from clone CH211-145O7 in ...    32   2.3    2
(CT661656) Danio rerio EST, clone ZF_mu_123c19 3'.                 32   3.1    2
(CT033796) Zebrafish DNA sequence from clone CH73-95A24 in l...    42   4.6    1
(AM472113) Vitis vinifera, whole genome shotgun sequence, co...    42   4.6    1
(AC131481) Rattus norvegicus clone CH230-7F8, WORKING DRAFT ...    42   4.6    1
(AC096893) Rattus norvegicus clone CH230-7H6, *** SEQUENCING...    42   4.6    1
(AC231091) Bos taurus clone CH240-491J23, WORKING DRAFT SEQU...    42   4.6    1
(AC219820) Bos taurus clone CH240-320N1, WORKING DRAFT SEQUE...    42   4.6    1
(AC218272) Bos taurus clone CH240-289D22, WORKING DRAFT SEQU...    42   4.6    1
(ED565950) AUAC-aag81e03.b1 Ascaris suum whole genome shotgu...    42   4.6    1
(CC510996) CH240_354L19.T7 CHORI-240 Bos taurus genomic clon...    42   4.6    1
(BZ473768) BONMN70TR BO_1.6_2_KB_tot Brassica oleracea genom...    42   4.6    1
(ES325926) Ss_Rev2_27A04_T3 Reverse subtracted library from ...    42   4.6    1
(AM614897) Entamoeba invadens IP1 GSS, clone inv054a06.p1k.        34   6.6    2
(AL928838) Zebrafish DNA sequence from clone CH211-148F13.         30   8.4    2
(AL935041) Zebrafish DNA sequence from clone CH211-172J16.         30   8.4    2
(AM460138) Vitis vinifera contig VV78X196869.14, whole genom...    32   9.6    2

>(AY047364) Dictyostelium discoideum cAMP phosphodiesterase (PdeE)
           gene, complete cds.
          Length = 6540

 Score =  147 bits (74), Expect = 1e-31
 Identities = 88/95 (92%)
 Strand = Plus / Minus


Query: 35  aaaaatatatattacaattnatttatttattaaacnaatatattttnttagtatncaaaa 94
           ||||||||||||||||||| ||||||||||||||| |||||||||| ||||||| |||||
Sbjct: 327 aaaaatatatattacaatttatttatttattaaacgaatatattttcttagtatacaaaa 268


Query: 95  aancaatcaattaatagtnctattacttnaatttt 129
           || ||||||||||||||| ||||||||| ||||||
Sbjct: 267 aaacaatcaattaatagtactattactttaatttt 233

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 100,492,949
Number of extensions: 11271708
Number of successful extensions: 4042058
Number of sequences better than 10.0: 51
Length of query: 140
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 118
Effective length of database: 93,199,600,587
Effective search space: 10997552869266
Effective search space used: 10997552869266
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7. 8
Homology vs Protein 
Query= Contig-U13718-1 (Contig-U13718-1Q) /CSM_Contig/Contig-U13718-1Q.Seq.d
         (140 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 29,306,916
Number of extensions: 366670
Number of successful extensions: 9
Number of sequences better than 10.0: 0
Number of HSP's gapped: 9
Number of HSP's successfully gapped: 0
Length of query: 46
Length of database: 1,051,180,864
Length adjustment: 20
Effective length of query: 26
Effective length of database: 986,449,684
Effective search space: 25647691784
Effective search space used: 25647691784
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: 25 (14.2 bits)
PSORT 

 psg: 1.00  gvh: 0.47  alm: 0.23  top: 0.60  tms: 0.07  mit: 0.36  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: 1.00  tyr: 0.33  leu: 0.11  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 1.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 48.0 %: nuclear
	 28.0 %: cytoplasmic
	  8.0 %: Golgi
	  8.0 %: mitochondrial
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U13718-1 is nuc
VS (DIR, S) 0
VH (FL, L) 1
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) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0