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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-U03441-1
Contig ID Contig-U03441-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U03441-1 (Contig-U03441-1Q) /CSM_Contig/Contig-U03441-1Q.Seq.d
TCAACAACCAACACATCAATTACCAACAAGCAATACAACAATCTACAACC
TAAACAAAACTACTACTACTACTACNGGGTACTACGTACAAAACCTATCA
ATAAAATTACTACAAGCNATGGTACCAAGTTTCCAATTGCCAGTAGTATT
AGNAAATAATGGAACAATTANAATTATTACTATGGAACTGCAGAGGTAAT
CAATCNAGCCAACGCTAAGAATACCACACAGAAGAAACGATAAAAAGAAT
TGGCACTCACNTTAGCACTCCTA
Gap no gap
Contig length 273
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 2919039
End point 2918766
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U03441
List of clone(s) 

est1=SFC473Z,1,274
Translated Amino Acid sequence 
QQPTHQLPTSNTTIYNLNKTTTTTTGYYVQNLSIKLLQAMVPSFQLPVVLXNNGTIXIIT
MELQR*sixptlriphrrndkknwhsx*hs
Translated Amino Acid sequence (All Frames) 
Frame A:
sttntsitnkqynnlqpkqnyyyyyxvlrtkpinkittsxgtkfpiassixk*wnnxnyy
ygtaevinxanaknttqkkr*kelaltlall


Frame B:
QQPTHQLPTSNTTIYNLNKTTTTTTGYYVQNLSIKLLQAMVPSFQLPVVLXNNGTIXIIT
MELQR*sixptlriphrrndkknwhsx*hs


Frame C:
nnqhinyqqaiqqstt*tklllllxgttyktyq*nyykxwyqvsncq*y*ximeqlxlll
wncrgnqssqr*eyhteetikrigthxstp
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U03441-1 (Contig-U03441-1Q)
/CSM_Contig/Contig-U03441-1Q.Seq.d
         (273 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U03441-1 (Contig-U03441-1Q) /CSM_Contig/Conti...   325  1e-89
Contig-U14734-1 (Contig-U14734-1Q) /CSM_Contig/Conti...    34  0.073
Contig-U13915-1 (Contig-U13915-1Q) /CSM_Contig/Conti...    34  0.073
Contig-U10899-1 (Contig-U10899-1Q) /CSM_Contig/Conti...    32  0.29
Contig-U14147-1 (Contig-U14147-1Q) /CSM_Contig/Conti...    30  1.1
Contig-U11141-1 (Contig-U11141-1Q) /CSM_Contig/Conti...    30  1.1
Contig-U05408-1 (Contig-U05408-1Q) /CSM_Contig/Conti...    30  1.1
Contig-U14905-1 (Contig-U14905-1Q) /CSM_Contig/Conti...    28  4.5
Contig-U14635-1 (Contig-U14635-1Q) /CSM_Contig/Conti...    28  4.5
Contig-U13978-1 (Contig-U13978-1Q) /CSM_Contig/Conti...    28  4.5

>Contig-U03441-1 (Contig-U03441-1Q) /CSM_Contig/Contig-U03441-1Q.Seq.d
          Length = 273

 Score =  325 bits (164), Expect = 1e-89
 Identities = 179/179 (100%)
 Strand = Plus / Plus

                                                                       
Query: 95  ctatcaataaaattactacaagcnatggtaccaagtttccaattgccagtagtattagna 154
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 95  ctatcaataaaattactacaagcnatggtaccaagtttccaattgccagtagtattagna 154

                                                                       
Query: 155 aataatggaacaattanaattattactatggaactgcagaggtaatcaatcnagccaacg 214
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 155 aataatggaacaattanaattattactatggaactgcagaggtaatcaatcnagccaacg 214

                                                                      
Query: 215 ctaagaataccacacagaagaaacgataaaaagaattggcactcacnttagcactccta 273
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 215 ctaagaataccacacagaagaaacgataaaaagaattggcactcacnttagcactccta 273


>Contig-U14734-1 (Contig-U14734-1Q) /CSM_Contig/Contig-U14734-1Q.Seq.d
          Length = 712

 Score = 34.2 bits (17), Expect = 0.073
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 154 aaataatggaacaatta 170
           |||||||||||||||||
Sbjct: 274 aaataatggaacaatta 258


>Contig-U13915-1 (Contig-U13915-1Q) /CSM_Contig/Contig-U13915-1Q.Seq.d
          Length = 1720

 Score = 34.2 bits (17), Expect = 0.073
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 96   tatcaataaaattacta 112
            |||||||||||||||||
Sbjct: 1064 tatcaataaaattacta 1048


  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: 1649
Number of Sequences: 6905
Number of extensions: 1649
Number of successful extensions: 321
Number of sequences better than 10.0: 20
length of query: 273
length of database: 5,674,871
effective HSP length: 15
effective length of query: 258
effective length of database: 5,571,296
effective search space: 1437394368
effective search space used: 1437394368
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. 5.31
Homology vs DNA 
Query= Contig-U03441-1 (Contig-U03441-1Q) /CSM_Contig/Contig-U03441-1Q.Seq.d
         (273 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

(BJ399395) Dictyostelium discoideum cDNA clone:dds5b20, 3' e...   287   1e-73  1
(AC116984) Dictyostelium discoideum chromosome 2 map 2567470...   165   2e-53  3
(AF134171) Dictyostelium discoideum retrotransposon TRE3-C, ...   165   3e-53  3
(AC211108) Chlorocebus aethiops clone CH252-219N1, WORKING D...    44   2.6    1
(CJ448475) Macaca fascicularis mRNA, clone: QflA-13850, 5' e...    44   2.6    1

>(BJ399395) Dictyostelium discoideum cDNA clone:dds5b20, 3' end,
           single read.
          Length = 274

 Score =  287 bits (145), Expect = 1e-73
 Identities = 160/160 (100%)
 Strand = Plus / Minus


Query: 114 aagcnatggtaccaagtttccaattgccagtagtattagnaaataatggaacaattanaa 173
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 161 aagcnatggtaccaagtttccaattgccagtagtattagnaaataatggaacaattanaa 102


Query: 174 ttattactatggaactgcagaggtaatcaatcnagccaacgctaagaataccacacagaa 233
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 101 ttattactatggaactgcagaggtaatcaatcnagccaacgctaagaataccacacagaa 42


Query: 234 gaaacgataaaaagaattggcactcacnttagcactccta 273
           ||||||||||||||||||||||||||||||||||||||||
Sbjct: 41  gaaacgataaaaagaattggcactcacnttagcactccta 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 127,804,997
Number of extensions: 6583659
Number of successful extensions: 403235
Number of sequences better than 10.0: 5
Length of query: 273
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 250
Effective length of database: 99,442,330,388
Effective search space: 24860582597000
Effective search space used: 24860582597000
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.28
Homology vs Protein 
Query= Contig-U03441-1 (Contig-U03441-1Q) /CSM_Contig/Contig-U03441-1Q.Seq.d
         (273 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AF134171_2(AF134171|pid:none) Dictyostelium discoideum retrotran...    50   3e-05
AF134171_1(AF134171|pid:none) Dictyostelium discoideum retrotran...    44   0.002
CP000383_422(CP000383|pid:none) Cytophaga hutchinsonii ATCC 3340...    32   7.1

>AF134171_2(AF134171|pid:none) Dictyostelium discoideum
           retrotransposon TRE3-C, complete sequence.
          Length = 1147

 Score = 49.7 bits (117), Expect = 3e-05
 Identities = 25/33 (75%), Positives = 27/33 (81%)
 Frame = +3

Query: 159 MEQLXLLLWNCRGNQSSQR*EYHTEETIKRIGT 257
           MEQL LLLWNCRGNQS+   +  TEETIKRIGT
Sbjct: 1   MEQLKLLLWNCRGNQSTNA-KNKTEETIKRIGT 32

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: 367,868,845
Number of extensions: 5430195
Number of successful extensions: 10524
Number of sequences better than 10.0: 3
Number of HSP's gapped: 10507
Number of HSP's successfully gapped: 3
Length of query: 91
Length of database: 1,061,185,681
Length adjustment: 60
Effective length of query: 31
Effective length of database: 865,078,801
Effective search space: 26817442831
Effective search space used: 26817442831
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: 0.81  gvh: 0.50  alm: 0.38  top: 0.53  tms: 0.00  mit: 0.43  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 

	 44.0 %: mitochondrial
	 40.0 %: nuclear
	 12.0 %: cytoplasmic
	  4.0 %: cytoskeletal

>> prediction for Contig-U03441-1 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) 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