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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-U04350-1
Contig ID Contig-U04350-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04350-1 (Contig-U04350-1Q) /CSM_Contig/Contig-U04350-1Q.Seq.d
TATCCCTATAGATAGAGTGACACAGCTACAGGATATATACATTTTTGAGA
CAGCGATTAACCAAACAGTATCAAATATACAAAAGAAAAAAAAGAACTAT
TTTCGAGTCTCATTGGTGTTATTAACCTTACTAATTATATCATTAGTATG
GTGTTTTTCAAAATATAAATTACAACAACAAGAATTCATTATAAATAATG
GAAATAATAGTAACATTCAACAACTACAACAACAACAACAATTAAATAAT
TTAGATTCAACAACAATATATACAACAAATGATAATGGAGACATTAATTT
TCATAATGACAATAATAATAATAAT
Gap no gap
Contig length 325
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 2731253
End point 2731578
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U04350
List of clone(s) 

est1=SSA281F,1,326
Translated Amino Acid sequence 
IPIDRVTQLQDIYIFETAINQTVSNIQKKKKNYFRVSLVLLTLLIISLVWCFSKYKLQQQ
EFIINNGNNSNIQQLQQQQQLNNLDSTTIYTTNDNGDINFHNDNNNNN
Translated Amino Acid sequence (All Frames) 
Frame A:
ypyr*sdtatgyihf*dsd*pnsikytkekkelfssligvinltnyiismvffki*ittt
rihyk*wk***hstttttttik*frfnnniynk**wrh*fs**q****


Frame B:
IPIDRVTQLQDIYIFETAINQTVSNIQKKKKNYFRVSLVLLTLLIISLVWCFSKYKLQQQ
EFIINNGNNSNIQQLQQQQQLNNLDSTTIYTTNDNGDINFHNDNNNNN


Frame C:
sl*ie*hsyriytflrqrltkqyqiykrkkrtifeshwcy*py*lyh*ygvfqninynnk
nsl*imeiivtfnnynnnnn*ii*iqqqyiqqmimetlifimtiiii
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04350-1 (Contig-U04350-1Q)
/CSM_Contig/Contig-U04350-1Q.Seq.d
         (325 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04350-1 (Contig-U04350-1Q) /CSM_Contig/Conti...   383  e-107
Contig-U13531-1 (Contig-U13531-1Q) /CSM_Contig/Conti...    46  2e-05
Contig-U05709-1 (Contig-U05709-1Q) /CSM_Contig/Conti...    44  9e-05
Contig-U09112-1 (Contig-U09112-1Q) /CSM_Contig/Conti...    42  4e-04
Contig-U05862-1 (Contig-U05862-1Q) /CSM_Contig/Conti...    42  4e-04
Contig-U13711-1 (Contig-U13711-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U14704-1 (Contig-U14704-1Q) /CSM_Contig/Conti...    34  0.088
Contig-U11036-1 (Contig-U11036-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U14060-1 (Contig-U14060-1Q) /CSM_Contig/Conti...    30  1.4
Contig-U12823-1 (Contig-U12823-1Q) /CSM_Contig/Conti...    30  1.4

>Contig-U04350-1 (Contig-U04350-1Q) /CSM_Contig/Contig-U04350-1Q.Seq.d
          Length = 325

 Score =  383 bits (193), Expect = e-107
 Identities = 209/217 (96%)
 Strand = Plus / Plus

                                                                       
Query: 1   tatccctatagatagagtgacacagctacaggatatatacatttttgagacagcgattaa 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   tatccctatagatagagtgacacagctacaggatatatacatttttgagacagcgattaa 60

                                                                       
Query: 61  ccaaacagtatcaaatatacaaaagnnnnnnnngaactattttcgagtctcattggtgtt 120
           |||||||||||||||||||||||||        |||||||||||||||||||||||||||
Sbjct: 61  ccaaacagtatcaaatatacaaaagaaaaaaaagaactattttcgagtctcattggtgtt 120

                                                                       
Query: 121 attaaccttactaattatatcattagtatggtgtttttcaaaatataaattacaacaaca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 attaaccttactaattatatcattagtatggtgtttttcaaaatataaattacaacaaca 180

                                                
Query: 181 agaattcattataaataatggaaataatagtaacatt 217
           |||||||||||||||||||||||||||||||||||||
Sbjct: 181 agaattcattataaataatggaaataatagtaacatt 217


 Score = 93.7 bits (47), Expect = 1e-19
 Identities = 47/47 (100%)
 Strand = Plus / Plus

                                                          
Query: 279 atgataatggagacattaattttcataatgacaataataataataat 325
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 279 atgataatggagacattaattttcataatgacaataataataataat 325


>Contig-U13531-1 (Contig-U13531-1Q) /CSM_Contig/Contig-U13531-1Q.Seq.d
          Length = 1758

 Score = 46.1 bits (23), Expect = 2e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                  
Query: 303 ataatgacaataataataataat 325
           |||||||||||||||||||||||
Sbjct: 887 ataatgacaataataataataat 909


 Score = 32.2 bits (16), Expect = 0.35
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                            
Query: 310  caataataataataat 325
            ||||||||||||||||
Sbjct: 1108 caataataataataat 1123


 Score = 32.2 bits (16), Expect = 0.35
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                               
Query: 165 ataaattacaacaacaagaa 184
           ||||||||||||| ||||||
Sbjct: 308 ataaattacaacatcaagaa 327


 Score = 30.2 bits (15), Expect = 1.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 311 aataataataataat 325
           |||||||||||||||
Sbjct: 283 aataataataataat 297


 Score = 30.2 bits (15), Expect = 1.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 311 aataataataataat 325
           |||||||||||||||
Sbjct: 280 aataataataataat 294


 Score = 30.2 bits (15), Expect = 1.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 311 aataataataataat 325
           |||||||||||||||
Sbjct: 898 aataataataataat 912


 Score = 28.2 bits (14), Expect = 5.4
 Identities = 20/22 (90%)
 Strand = Plus / Plus

                                 
Query: 302 cataatgacaataataataata 323
           |||||| | |||||||||||||
Sbjct: 277 cataataataataataataata 298


 Score = 28.2 bits (14), Expect = 5.4
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 311 aataataataataa 324
           ||||||||||||||
Sbjct: 901 aataataataataa 914


 Score = 28.2 bits (14), Expect = 5.4
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 312 ataataataataat 325
           ||||||||||||||
Sbjct: 278 ataataataataat 291


 Score = 28.2 bits (14), Expect = 5.4
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 168 aattacaacaacaa 181
           ||||||||||||||
Sbjct: 59  aattacaacaacaa 72


>Contig-U05709-1 (Contig-U05709-1Q) /CSM_Contig/Contig-U05709-1Q.Seq.d
          Length = 593

 Score = 44.1 bits (22), Expect = 9e-05
 Identities = 28/30 (93%)
 Strand = Plus / Plus

                                         
Query: 296 aattttcataatgacaataataataataat 325
           |||||||| ||||| |||||||||||||||
Sbjct: 423 aattttcaaaatgaaaataataataataat 452


 Score = 30.2 bits (15), Expect = 1.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 311 aataataataataat 325
           |||||||||||||||
Sbjct: 45  aataataataataat 59


 Score = 30.2 bits (15), Expect = 1.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 311 aataataataataat 325
           |||||||||||||||
Sbjct: 42  aataataataataat 56


 Score = 30.2 bits (15), Expect = 1.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 311 aataataataataat 325
           |||||||||||||||
Sbjct: 39  aataataataataat 53


 Score = 30.2 bits (15), Expect = 1.4
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 311 aataataataataat 325
           |||||||||||||||
Sbjct: 36  aataataataataat 50


 Score = 28.2 bits (14), Expect = 5.4
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 311 aataataataataa 324
           ||||||||||||||
Sbjct: 441 aataataataataa 454


  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: 20,459
Number of Sequences: 6905
Number of extensions: 20459
Number of successful extensions: 10123
Number of sequences better than 10.0: 1857
length of query: 325
length of database: 5,674,871
effective HSP length: 15
effective length of query: 310
effective length of database: 5,571,296
effective search space: 1727101760
effective search space used: 1727101760
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. 6.17
Homology vs DNA 
Query= Contig-U04350-1 (Contig-U04350-1Q) /CSM_Contig/Contig-U04350-1Q.Seq.d
         (325 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

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

(AU075115) Dictyostelium discoideum slug cDNA, clone SSA281.      234   e-102  2
(CR931725) Zebrafish DNA sequence from clone DKEY-22M10 in l...    48   0.20   1
(CR376730) Zebrafish DNA sequence from clone CH211-205A14 in...    48   0.20   1
(BX511087) Zebrafish DNA sequence from clone DKEY-261O7 in l...    48   0.20   1
(BX000477) Zebrafish DNA sequence from clone CH211-59D8 in l...    48   0.20   1
(CT573153) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    48   0.20   1
(ED634565) GM_WBa0039M08.r GM_WBa Glycine max genomic clone ...    46   0.80   1
(BX005374) Zebrafish DNA sequence from clone DKEY-29H23 in l...    40   1.2    3
(CU062580) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    36   3.2    4
(CR450780) Zebrafish DNA sequence from clone DKEY-160G21 in ...    44   3.2    1
(BX927336) Zebrafish DNA sequence from clone CH211-215P11 in...    44   3.2    1
(BX248105) Zebrafish DNA sequence from clone CH211-270A9.          44   3.2    1
(AL807378) Zebrafish DNA sequence from clone CH211-215A18 in...    44   3.2    1
(EU677193) Oedogonium cardiacum strain SAG 575-1b chloroplas...    44   3.2    1
(EF587367) Oedogonium cardiacum strain SAG 575-1b RNA polyme...    44   3.2    1
(FB728186) Sequence 669 from Patent WO2003013533.                  44   3.2    1
(DD156891) Means and methods for improved treatment of cance...    44   3.2    1
(DD156339) Means and methods for improved treatment of cance...    44   3.2    1
(DD144751) Means and methods for improved treatment of cance...    44   3.2    1
(DD142682) Means and methods for improved treatment of cance...    44   3.2    1
(DD134580) Means and methods for improved treatment of cance...    44   3.2    1
(CS623051) Sequence 669 from Patent WO2003013537.                  44   3.2    1
(AX707901) Sequence 669 from Patent WO03013536.                    44   3.2    1
(AX706971) Sequence 669 from Patent WO03013534.                    44   3.2    1
(AC025277) Homo sapiens chromosome 16 clone CTD-3229J4, comp...    44   3.2    1
(FP236631) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   3.2    1
(AC224057) Bos taurus clone CH240-451E9, WORKING DRAFT SEQUE...    44   3.2    1
(ER843581) PPTB692TR Solanum tuberosum RHPOTKEY BAC ends Sol...    44   3.2    1
(EK331520) 1095467025697 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.2    1
(EK121617) 1092963543347 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.2    1
(EK120737) 1092963368433 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.2    1
(EK065294) 1092960113786 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.2    1
(EH762797) CNSL8799.b1_N16.ab1 CNS(LMS) yellow starthistle C...    44   3.2    1
(BG603106) EST502196 Plasmodium yoelii sporozoite cDNA Plasm...    44   3.2    1
(BX957361) Zebrafish DNA sequence from clone DKEY-269O24 in ...    40   5.6    2
(CP000817) Lysinibacillus sphaericus C3-41, complete genome.       40   5.9    8
(AC144656) Medicago truncatula clone mth2-27d4, complete seq...    32   6.1    2
(AC158464) Medicago truncatula chromosome 2 clone mth2-145m2...    32   6.2    2
(AC183298) Pan troglodytes BAC clone CH251-330I21 from chrom...    36   6.8    4
(CU855786) Zebrafish DNA sequence from clone CH1073-504D15 i...    40   6.8    2
(EK244464) 1095460247096 Global-Ocean-Sampling_GS-31-01-01-1...    30   8.0    2
(CG948513) MBECP14TF mth2 Medicago truncatula genomic clone ...    32   8.0    2
(EJ999013) 1093025006812 Global-Ocean-Sampling_GS-30-02-01-1...    30   8.0    2
(EJ996716) 1093024000668 Global-Ocean-Sampling_GS-30-02-01-1...    30   8.1    2
(AC150374) Colobus guereza clone CH272-220M2, WORKING DRAFT ...    42   9.8    2

>(AU075115) Dictyostelium discoideum slug cDNA, clone SSA281.
          Length = 240

 Score =  234 bits (118), Expect(2) = e-102
 Identities = 118/118 (100%)
 Strand = Plus / Plus


Query: 94  gaactattttcgagtctcattggtgttattaaccttactaattatatcattagtatggtg 153
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 94  gaactattttcgagtctcattggtgttattaaccttactaattatatcattagtatggtg 153


Query: 154 tttttcaaaatataaattacaacaacaagaattcattataaataatggaaataatagt 211
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 154 tttttcaaaatataaattacaacaacaagaattcattataaataatggaaataatagt 211

 Score =  168 bits (85), Expect(2) = e-102
 Identities = 85/85 (100%)
 Strand = Plus / Plus


Query: 1  tatccctatagatagagtgacacagctacaggatatatacatttttgagacagcgattaa 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  tatccctatagatagagtgacacagctacaggatatatacatttttgagacagcgattaa 60


Query: 61 ccaaacagtatcaaatatacaaaag 85
          |||||||||||||||||||||||||
Sbjct: 61 ccaaacagtatcaaatatacaaaag 85

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 271,938,633
Number of extensions: 18542242
Number of successful extensions: 1545371
Number of sequences better than 10.0: 45
Length of query: 325
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 302
Effective length of database: 99,442,330,388
Effective search space: 30031583777176
Effective search space used: 30031583777176
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04350-1 (Contig-U04350-1Q) /CSM_Contig/Contig-U04350-1Q.Seq.d
         (325 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 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: 3268448
Number of Hits to DB: 332,674,952
Number of extensions: 4654573
Number of successful extensions: 23960
Number of sequences better than 10.0: 0
Number of HSP's gapped: 23959
Number of HSP's successfully gapped: 0
Length of query: 108
Length of database: 1,061,185,681
Length adjustment: 76
Effective length of query: 32
Effective length of database: 812,783,633
Effective search space: 26009076256
Effective search space used: 26009076256
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: 0.75  gvh: 0.83  alm: 0.18  top: 0.27  tms: 0.07  mit: 0.29  mip: 0.00
 nuc: 0.04  erl: 0.00  erm: 0.60  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  tyr: 0.28  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 : 1.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 32.0 %: mitochondrial
	 20.0 %: Golgi
	 16.0 %: nuclear
	 12.0 %: cytoplasmic
	  8.0 %: endoplasmic reticulum
	  4.0 %: extracellular, including cell wall
	  4.0 %: vacuolar
	  4.0 %: peroxisomal

>> prediction for Contig-U04350-1 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) 1
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