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Dicty_cDB
Contig List | Clone List | cDNA Library List
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U05481-1
Contig ID Contig-U05481-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U05481-1 (Contig-U05481-1Q) /CSM_Contig/Contig-U05481-1Q.Seq.d
GTAGATTAATTTCTCCCTATGAAACACCTTCCGACCTTTATATGAATGAT
AGTGATNTAATCCTTGCCNCTNGAATTNTTCNNCNCNAATAANGGNAATT
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAATAAT
ACATAAACAAANTTAAAATATGAAACNTTNNAAACCAAANTTGATAACAA
CAANTAAAATATAANTTGGNTCAATAAACTTGANTCAAAGANGANTAATA
ATAATAANTTATATTTTTATTATTTNATTAAAAAANAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAANTAAANTNTNNGTNTTTATATGTCATAA
Gap no gap
Contig length 344
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 U05481
List of clone(s) 

est1=SSI707E,1,345
Translated Amino Acid sequence 
vd*flpmkhlptfi*mivx*slplexfxxnxgn*kkkkkkkkkkkkkrnnt*txlkyetx
xtkxdnnx*NIXWXNKLXSKXXNNNXLYFYYXIKKXKKKKKKKKKXKXXVFICH
Translated Amino Acid sequence (All Frames) 
Frame A:
vd*flpmkhlptfi*mivx*slplexfxxnxgn*kkkkkkkkkkkkkrnnt*txlkyetx
xtkxdnnx*NIXWXNKLXSKXXNNNXLYFYYXIKKXKKKKKKKKKXKXXVFICH


Frame B:
*infsl*ntfrplye***xnpcxxnxsxxixxikkkkkkkkkkkkkkeiihkqx*nmkxx
kpxlittxki*xgsinlxqrxxiiixyifiixlkxkkkkkkkkkkxxxxxlyvi


Frame C:
rlispyetpsdlymndsdxilaxxixxxx*xxlkkkkkkkkkkkkkkk*yinkxki*nxx
nqx**qqxkyxlxq*t*xkxx****xifllfx*kxkkkkkkkkkx*xxxxyms*
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05481-1 (Contig-U05481-1Q)
/CSM_Contig/Contig-U05481-1Q.Seq.d
         (344 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05481-1 (Contig-U05481-1Q) /CSM_Contig/Conti...   194  4e-50
Contig-U01680-1 (Contig-U01680-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U11421-1 (Contig-U11421-1Q) /CSM_Contig/Conti...    36  0.024
Contig-U12196-1 (Contig-U12196-1Q) /CSM_Contig/Conti...    34  0.093
Contig-U11680-1 (Contig-U11680-1Q) /CSM_Contig/Conti...    34  0.093
Contig-U09190-1 (Contig-U09190-1Q) /CSM_Contig/Conti...    34  0.093
Contig-U06281-1 (Contig-U06281-1Q) /CSM_Contig/Conti...    34  0.093
Contig-U03396-1 (Contig-U03396-1Q) /CSM_Contig/Conti...    34  0.093
Contig-U14904-1 (Contig-U14904-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U14821-1 (Contig-U14821-1Q) /CSM_Contig/Conti...    32  0.37

>Contig-U05481-1 (Contig-U05481-1Q) /CSM_Contig/Contig-U05481-1Q.Seq.d
          Length = 344

 Score =  194 bits (98), Expect = 4e-50
 Identities = 137/137 (100%)
 Strand = Plus / Plus

                                                                       
Query: 143 gaaataatacataaacaaanttaaaatatgaaacnttnnaaaccaaanttgataacaaca 202
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 143 gaaataatacataaacaaanttaaaatatgaaacnttnnaaaccaaanttgataacaaca 202

                                                                       
Query: 203 antaaaatataanttggntcaataaacttgantcaaagangantaataataataanttat 262
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203 antaaaatataanttggntcaataaacttgantcaaagangantaataataataanttat 262

                            
Query: 263 atttttattatttnatt 279
           |||||||||||||||||
Sbjct: 263 atttttattatttnatt 279


 Score =  139 bits (70), Expect = 2e-33
 Identities = 100/100 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   gtagattaatttctccctatgaaacaccttccgacctttatatgaatgatagtgatntaa 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gtagattaatttctccctatgaaacaccttccgacctttatatgaatgatagtgatntaa 60

                                                   
Query: 61  tccttgccnctngaattnttcnncncnaataanggnaatt 100
           ||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tccttgccnctngaattnttcnncncnaataanggnaatt 100


 Score = 28.2 bits (14), Expect = 5.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 331 tttatatgtcataa 344
           ||||||||||||||
Sbjct: 331 tttatatgtcataa 344


>Contig-U01680-1 (Contig-U01680-1Q) /CSM_Contig/Contig-U01680-1Q.Seq.d
          Length = 1102

 Score = 40.1 bits (20), Expect = 0.002
 Identities = 22/23 (95%)
 Strand = Plus / Minus

                                  
Query: 249 taataataanttatatttttatt 271
           ||||||||| |||||||||||||
Sbjct: 157 taataataatttatatttttatt 135


>Contig-U11421-1 (Contig-U11421-1Q) /CSM_Contig/Contig-U11421-1Q.Seq.d
          Length = 1479

 Score = 36.2 bits (18), Expect = 0.024
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                 
Query: 259  ttatatttttattatttnatt 279
            ||||||||||||||||| |||
Sbjct: 1458 ttatatttttattattttatt 1438


  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: 15,150
Number of Sequences: 6905
Number of extensions: 15150
Number of successful extensions: 874
Number of sequences better than 10.0: 266
length of query: 344
length of database: 5,674,871
effective HSP length: 15
effective length of query: 329
effective length of database: 5,571,296
effective search space: 1832956384
effective search space used: 1832956384
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. 7.22
Homology vs DNA 
Query= Contig-U05481-1 (Contig-U05481-1Q) /CSM_Contig/Contig-U05481-1Q.Seq.d
         (344 letters)

Database: ddbj_B
           105,743,758 sequences; 104,622,809,269 total letters

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

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

(AU073907) Dictyostelium discoideum slug cDNA, clone SSI707.      141   3e-64  2
(C90546) Dictyostelium discoideum slug cDNA, clone SSI707.        194   2e-50  3
(BX470150) Zebrafish DNA sequence from clone DKEY-164K14 in ...    46   0.88   1
(AE014187) Plasmodium falciparum 3D7 chromosome 14, complete...    46   0.88   1
(AC117076) Dictyostelium discoideum chromosome 2 map 3323568...    46   0.88   1
(AL591173) Human DNA sequence from clone RP11-316O2 on chrom...    46   0.88   1
(DU642634) Ciuffi-HIV-293T-siScram-33D09.revQ=50 Human Integ...    46   0.88   1
(CU464123) Zebrafish DNA sequence from clone DKEY-110I1 in l...    44   3.5    1
(CT583719) Zebrafish DNA sequence from clone DKEY-112E7 in l...    44   3.5    1
(CR388075) Zebrafish DNA sequence from clone DKEY-223L3 in l...    44   3.5    1
(CR381585) Zebrafish DNA sequence from clone DKEY-27P7 in li...    44   3.5    1
(AP008215) Oryza sativa (japonica cultivar-group) genomic DN...    44   3.5    1
(AP006548) Oryza sativa Japonica Group genomic DNA, chromoso...    44   3.5    1
(AK109723) Oryza sativa Japonica Group cDNA clone:002-146-B0...    44   3.5    1
(AR659612) Sequence 653 from patent US 6900016.                    44   3.5    1
(AP006249) Homo sapiens genomic DNA, chromosome 8, clone:RP1...    44   3.5    1
(AC087273) Homo sapiens chromosome 8, clone RP11-156K13, com...    44   3.5    1
(AC027117) Homo sapiens chromosome 8, clone RP11-806O11, com...    44   3.5    1
(AC149980) Strongylocentrotus purpuratus clone R3-32A6, WORK...    44   3.5    1
(AC120292) Rattus norvegicus clone CH230-239B15, WORKING DRA...    44   3.5    1
(AC103000) Rattus norvegicus clone CH230-192M3, WORKING DRAF...    44   3.5    1
(FP102031) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   3.5    1
(AC026854) Homo sapiens chromosome 8 clone RP11-156K13, WORK...    44   3.5    1
(CT027709) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   3.5    1
(AF267167) Homo sapiens chromosome 8 clone CTD-2033H15 map 8...    44   3.5    1
(AC201294) Strongylocentrotus purpuratus clone R3-16G8, WORK...    44   3.5    1
(AC180743) Strongylocentrotus purpuratus clone R3-3083B11, W...    44   3.5    1
(AC180493) Strongylocentrotus purpuratus clone R3-30F17, WOR...    44   3.5    1
(AC179146) Strongylocentrotus purpuratus clone R3-4012D3, WO...    44   3.5    1
(AC176800) Strongylocentrotus purpuratus clone R3-1110K11, W...    44   3.5    1
(DE592149) Bombyx mori genomic DNA, Fosmid clone:GBMFno246_k...    44   3.5    1
(CU818434) A BAC library has been constructed from PN40024 g...    44   3.5    1
(BH714635) BOHYL79TR BO_2_3_KB Brassica oleracea genomic clo...    44   3.5    1
(CI199930) Oryza sativa Japonica Group cDNA, clone: 037-M016...    44   3.5    1
(CI142941) Oryza sativa Japonica Group cDNA, clone: 028-M035...    44   3.5    1
(EY392537) CAXA9861.rev CAXA Helobdella robusta Subtracted L...    44   3.5    1
(EY374324) CAXA15017.rev CAXA Helobdella robusta Subtracted ...    44   3.5    1
(AC218607) Bos taurus clone CH240-302I23, WORKING DRAFT SEQU...    42   4.7    2
(AX346209) Sequence 1280 from Patent WO0200928.                    42   6.4    2
(FB571382) Sequence 249 from Patent EP1865317.                     32   6.5    2
(FB571326) Sequence 193 from Patent EP1865317.                     32   6.5    2

>(AU073907) Dictyostelium discoideum slug cDNA, clone SSI707.
          Length = 240

 Score =  141 bits (71), Expect(2) = 3e-64
 Identities = 89/98 (90%)
 Strand = Plus / Plus


Query: 143 gaaataatacataaacaaanttaaaatatgaaacnttnnaaaccaaanttgataacaaca 202
           ||||||||||||||||||| |||||||||||||| ||  |||||||| ||||||||||||
Sbjct: 143 gaaataatacataaacaaatttaaaatatgaaactttaaaaaccaaatttgataacaaca 202


Query: 203 antaaaatataanttggntcaataaacttgantcaaag 240
           | |||||||||| |||| ||||||||||||| ||||||
Sbjct: 203 attaaaatataatttggttcaataaacttgattcaaag 240

 Score =  139 bits (70), Expect(2) = 3e-64
 Identities = 90/100 (90%)
 Strand = Plus / Plus


Query: 1   gtagattaatttctccctatgaaacaccttccgacctttatatgaatgatagtgatntaa 60
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct: 1   gtagattaatttctccctatgaaacaccttccgacctttatatgaatgatagtgatataa 60


Query: 61  tccttgccnctngaattnttcnncncnaataanggnaatt 100
           |||||||| || ||||| |||  | | ||||| || ||||
Sbjct: 61  tccttgcctctagaattattcaacacaaataaaggaaatt 100

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 218,427,895
Number of extensions: 19715694
Number of successful extensions: 1044695
Number of sequences better than 10.0: 41
Length of query: 344
Length of database: 104,622,809,269
Length adjustment: 23
Effective length of query: 321
Effective length of database: 102,190,702,835
Effective search space: 32803215610035
Effective search space used: 32803215610035
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 8. 1
Homology vs Protein 
Query= Contig-U05481-1 (Contig-U05481-1Q) /CSM_Contig/Contig-U05481-1Q.Seq.d
         (344 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: 190,000,326
Number of extensions: 1678114
Number of successful extensions: 1187
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1184
Number of HSP's successfully gapped: 0
Length of query: 114
Length of database: 1,061,185,681
Length adjustment: 81
Effective length of query: 33
Effective length of database: 796,441,393
Effective search space: 26282565969
Effective search space used: 26282565969
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: 0.83  gvh: 0.18  alm: 0.66  top: 0.53  tms: 0.00  mit: 0.38  mip: 0.00
 nuc: 0.49  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 

	 84.0 %: nuclear
	  8.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U05481-1 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) 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