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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-U08553-1
Contig ID Contig-U08553-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U08553-1 (Contig-U08553-1Q) /CSM_Contig/Contig-U08553-1Q.Seq.d
NNNNNNNNNNCCNATTGGNGNATTAGNATTNAAANAAAATCNATCNATTG
ATTTAATTTAATTNCAAAANGAAATTAATAANATCCTTACCCNANATATT
GAATCATGGGCNGTCTTAANAAAAATTTTNATTGNTAACCNATTACCNAA
AACNAAAGNTGGNAAAANTCCNANACTAATTTTGNCNAATTTATTAAATG
ATTCNAATTANCNACNACCC
Gap no gap
Contig length 220
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 U08553
List of clone(s) 

est1=SFI555Z,1,211
Translated Amino Acid sequence 
xxxpigxlxxkxnxsidli*XQXEINXILTXXIESWAVLXKIXIXNXLPKTKXGKXPXLI
LXNLLNDSNXXXP
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxxwxixixxksix*fnlixkxn**xpypxy*imgxlxknfxx*pitxnxxwxxsxtn
fxxfik*fxlxtt


Frame B:
xxxpigxlxxkxnxsidli*XQXEINXILTXXIESWAVLXKIXIXNXLPKTKXGKXPXLI
LXNLLNDSNXXXP


Frame C:
xxxxlxx*xxxkixxli*fnxkxklixslpxilnhgxs*xkfxlxtxyxkxkxxkxxx*f
xxiy*mixixxx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U08553-1 (Contig-U08553-1Q)
/CSM_Contig/Contig-U08553-1Q.Seq.d
         (220 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U08553-1 (Contig-U08553-1Q) /CSM_Contig/Conti...   168  2e-42
Contig-U11360-1 (Contig-U11360-1Q) /CSM_Contig/Conti...    68  4e-12
Contig-U12862-1 (Contig-U12862-1Q) /CSM_Contig/Conti...    46  2e-05
Contig-U10251-1 (Contig-U10251-1Q) /CSM_Contig/Conti...    32  0.23
Contig-U05051-1 (Contig-U05051-1Q) /CSM_Contig/Conti...    32  0.23
Contig-U14861-1 (Contig-U14861-1Q) /CSM_Contig/Conti...    30  0.91
Contig-U14682-1 (Contig-U14682-1Q) /CSM_Contig/Conti...    30  0.91
Contig-U14399-1 (Contig-U14399-1Q) /CSM_Contig/Conti...    30  0.91
Contig-U13945-1 (Contig-U13945-1Q) /CSM_Contig/Conti...    30  0.91
Contig-U09790-1 (Contig-U09790-1Q) /CSM_Contig/Conti...    30  0.91

>Contig-U08553-1 (Contig-U08553-1Q) /CSM_Contig/Contig-U08553-1Q.Seq.d
          Length = 220

 Score =  168 bits (85), Expect = 2e-42
 Identities = 171/178 (96%)
 Strand = Plus / Plus

                                                                       
Query: 43  atcnattgatttaatttaattncaaaangaaattaataanatccttacccnanatattga 102
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 43  atcnattgatttaatttaattncaaaangaaattaataanatccttacccnanatattga 102

                                                                       
Query: 103 atcatgggcngtcttnnnnnnnnttttnattgntaaccnattaccnaaaacnaaagntgg 162
           |||||||||||||||  |     |||||||||||||||||||||||||||||||||||||
Sbjct: 103 atcatgggcngtcttaanaaaaattttnattgntaaccnattaccnaaaacnaaagntgg 162

                                                                     
Query: 163 naaaantccnanactaattttgncnaatttattaaatgattcnaattancnacnaccc 220
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 163 naaaantccnanactaattttgncnaatttattaaatgattcnaattancnacnaccc 220


>Contig-U11360-1 (Contig-U11360-1Q) /CSM_Contig/Contig-U11360-1Q.Seq.d
          Length = 3470

 Score = 67.9 bits (34), Expect = 4e-12
 Identities = 108/141 (76%)
 Strand = Plus / Plus

                                                                        
Query: 43   atcnattgatttaatttaattncaaaangaaattaataanatccttacccnanatattga 102
            ||| |||||||||| | |||| ||||| ||||||||||| ||| | || | | |||||||
Sbjct: 2508 atcaattgatttaaataaattacaaaatgaaattaataatatcatcacgcaagatattga 2567

                                                                        
Query: 103  atcatgggcngtcttnnnnnnnnttttnattgntaaccnattaccnaaaacnaaagntgg 162
            ||||  ||| |||||        |||| |||| ||||| |||||| ||||| |||| |||
Sbjct: 2568 atcactggcagtcttaaaaaaaattttaattgttaaccaattaccaaaaacaaaagttgg 2627

                                 
Query: 163  naaaantccnanactaatttt 183
             |||| ||| | || ||||||
Sbjct: 2628 taaaattccaagacaaatttt 2648


 Score = 28.2 bits (14), Expect = 3.6
 Identities = 48/61 (78%)
 Strand = Plus / Plus

                                                                        
Query: 47   attgatttaatttaattncaaaangaaattaataanatccttacccnanatattgaatca 106
            |||||||||| | |||| ||||| ||||| ||| | ||  |||  | | |||||||||||
Sbjct: 3095 attgatttaaataaattacaaaatgaaataaattatataattaaacaagatattgaatca 3154

             
Query: 107  t 107
            |
Sbjct: 3155 t 3155


>Contig-U12862-1 (Contig-U12862-1Q) /CSM_Contig/Contig-U12862-1Q.Seq.d
          Length = 650

 Score = 46.1 bits (23), Expect = 2e-05
 Identities = 37/43 (86%)
 Strand = Plus / Plus

                                                      
Query: 43  atcnattgatttaatttaattncaaaangaaattaataanatc 85
           ||| |||||||||| | |||| ||||| ||||||||||| |||
Sbjct: 528 atcaattgatttaaataaattacaaaatgaaattaataatatc 570


 Score = 30.2 bits (15), Expect = 0.91
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 188 aatttattaaatgat 202
           |||||||||||||||
Sbjct: 572 aatttattaaatgat 586


  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: 1824
Number of Sequences: 6905
Number of extensions: 1824
Number of successful extensions: 653
Number of sequences better than 10.0: 37
length of query: 220
length of database: 5,674,871
effective HSP length: 15
effective length of query: 205
effective length of database: 5,571,296
effective search space: 1142115680
effective search space used: 1142115680
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 2008.11.13
Homology vs DNA 
Query= Contig-U08553-1 (Contig-U08553-1Q) /CSM_Contig/Contig-U08553-1Q.Seq.d
         (220 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

(BJ402912) Dictyostelium discoideum cDNA clone:dds18m13, 3' ...   232   4e-57  1
(AC116984) Dictyostelium discoideum chromosome 2 map 2567470...   200   1e-47  1
(BJ341319) Dictyostelium discoideum cDNA clone:dda6k04, 3' e...   190   1e-44  1
(BJ379606) Dictyostelium discoideum cDNA clone:ddc35m07, 3' ...   176   2e-40  1
(AU037827) Dictyostelium discoideum slug cDNA, clone SSE344.       76   1e-21  2
(BJ385744) Dictyostelium discoideum cDNA clone:ddc56c01, 3' ...    76   2e-10  2
(BJ374664) Dictyostelium discoideum cDNA clone:ddc9o18, 3' e...    76   5e-10  1
(BJ373595) Dictyostelium discoideum cDNA clone:ddc3g22, 3' e...    58   5e-07  2
(C93049) Dictyostelium discoideum slug cDNA, clone SSF633.         44   1.9    1
(AL513023) Human DNA sequence from clone RP11-256A6 on chrom...    42   7.7    1
(AC025979) Homo sapiens chromosome Y clone RP11-641B11 map Y...    42   7.7    1

>(BJ402912) Dictyostelium discoideum cDNA clone:dds18m13, 3' end,
           single read.
          Length = 211

 Score =  232 bits (117), Expect = 4e-57
 Identities = 207/207 (100%)
 Strand = Plus / Minus


Query: 14  attggngnattagnattnaaanaaaatcnatcnattgatttaatttaattncaaaangaa 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 208 attggngnattagnattnaaanaaaatcnatcnattgatttaatttaattncaaaangaa 149


Query: 74  attaataanatccttacccnanatattgaatcatgggcngtcttaanaaaaattttnatt 133
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 148 attaataanatccttacccnanatattgaatcatgggcngtcttaanaaaaattttnatt 89


Query: 134 gntaaccnattaccnaaaacnaaagntggnaaaantccnanactaattttgncnaattta 193
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 88  gntaaccnattaccnaaaacnaaagntggnaaaantccnanactaattttgncnaattta 29


Query: 194 ttaaatgattcnaattancnacnaccc 220
           |||||||||||||||||||||||||||
Sbjct: 28  ttaaatgattcnaattancnacnaccc 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 83,476,634
Number of extensions: 5542224
Number of successful extensions: 1160085
Number of sequences better than 10.0: 12
Length of query: 220
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 197
Effective length of database: 93,106,754,628
Effective search space: 18342030661716
Effective search space used: 18342030661716
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.24
Homology vs Protein 
Query= Contig-U08553-1 (Contig-U08553-1Q) /CSM_Contig/Contig-U08553-1Q.Seq.d
         (220 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116984_184(AC116984|pid:none) Dictyostelium discoideum chromos...    67   2e-10
AC116984_182(AC116984|pid:none) Dictyostelium discoideum chromos...    50   2e-05
AC116984_181(AC116984|pid:none) Dictyostelium discoideum chromos...    48   9e-05
AC116984_172(AC116984|pid:none) Dictyostelium discoideum chromos...    45   6e-04
AC116984_174(AC116984|pid:none) Dictyostelium discoideum chromos...    45   0.001
AC116984_173(AC116984|pid:none) Dictyostelium discoideum chromos...    44   0.002
AC116984_175(AC116984|pid:none) Dictyostelium discoideum chromos...    40   0.026

>AC116984_184(AC116984|pid:none) Dictyostelium discoideum chromosome
           2 map 2567470-3108875 strain AX4, complete sequence.
          Length = 634

 Score = 67.0 bits (162), Expect = 2e-10
 Identities = 39/70 (55%), Positives = 40/70 (57%)
 Frame = +2

Query: 11  PIGXLXXKXNXSIDLI*XQXEINXILTXXIESWAVLXKIXIXNXLPKTKXGKXPXXXXXX 190
           PIG L  K N SIDLI  Q EIN I+T  IES AVL KI I N LPKTK GK P
Sbjct: 556 PIGVLVLKENQSIDLIKLQNEINNIITQDIESCAVLRKILIVNQLPKTKVGKIPRLILSN 615

Query: 191 XXXDSNXXXP 220
              DSN   P
Sbjct: 616 LLNDSNYQLP 625

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: 3204285
Number of Hits to DB: 95,394,170
Number of extensions: 2065368
Number of successful extensions: 76
Number of sequences better than 10.0: 7
Number of HSP's gapped: 76
Number of HSP's successfully gapped: 7
Length of query: 73
Length of database: 1,040,966,779
Length adjustment: 44
Effective length of query: 29
Effective length of database: 899,978,239
Effective search space: 26099368931
Effective search space used: 26099368931
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: 27 (15.0 bits)
PSORT 

 psg: 0.75  gvh: 0.59  alm: 0.42  top: 0.53  tms: 0.00  mit: 0.17  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 

	 52.0 %: cytoplasmic
	 28.0 %: nuclear
	  8.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: Golgi

>> prediction for Contig-U08553-1 is cyt
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) 1
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0