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Dicty_cDB
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U07063-1
Contig ID Contig-U07063-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U07063-1 (Contig-U07063-1Q) /CSM_Contig/Contig-U07063-1Q.Seq.d
ATAAAAATTAATATAAAAAAAGCAACAACAACAATTTGTATACTAATTGG
AATTAAAGATTAAATTTACATGACAAGGATGGTGTTTTTTTTAATGAAAA
TAGTAAATAGTTTCACAATATTCACACTCACTTATATATAATAATTTTTA
TACACACCATAATTAATATATTTTACAATATAAATTCAATAAATTGAAAA
ACATATATAAAAAAAGTAATAATATTTTTGTTTTTATCTTTTCATATTTA
AACATTGCTAATAACAATTTCACATGGGAAAAAAAAACAAAACAAAACAA
AACAAAAAACAAAACATTTTAATTATTATTATTGNGNGGTATTGTCTAAA
AAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTNAAAAAAAA
Gap no gap
Contig length 396
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 5243640
End point 5243244
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U07063
List of clone(s) 

est1=VSK189F,1,397
est2=VSK189Z,1,315
Translated Amino Acid sequence 
*kli*kkqqqqfvy*lelkikft*qgwcff**k**ivsqyshsliynnfythhn*YILQY
KFNKLKNIYKKSNNIFVFIFSYLNIANNNFTWEKKTKQNKTKNKTF*llllxgiv*kkkk
kkkkkfffxkk
Translated Amino Acid sequence (All Frames) 
Frame A:
ikinikkattticiligikd*iymtrmvfflmkivnsftiftltyi**flytp*liyfti
*iq*iekhi*kk**yfcfylfifkhc**qfhmgkknktkqnkkqniliiiixxyclkkkk
kkkkkifffxkk


Frame B:
*kli*kkqqqqfvy*lelkikft*qgwcff**k**ivsqyshsliynnfythhn*YILQY
KFNKLKNIYKKSNNIFVFIFSYLNIANNNFTWEKKTKQNKTKNKTF*llllxgiv*kkkk
kkkkkfffxkk


Frame C:
kn*ykksnnnnlytnwn*rlnlhdkdgvffnensk*fhnihthlyiiifihtiinifyni
nsin*ktyikkviiflflsfhi*tllitishgkkkqnktkqktkhfnyyyxxvlskkkkk
kkkknfffxkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U07063-1 (Contig-U07063-1Q)
/CSM_Contig/Contig-U07063-1Q.Seq.d
         (396 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U07063-1 (Contig-U07063-1Q) /CSM_Contig/Conti...   168  3e-42
Contig-U14386-1 (Contig-U14386-1Q) /CSM_Contig/Conti...    36  0.027
Contig-U11851-1 (Contig-U11851-1Q) /CSM_Contig/Conti...    36  0.027
Contig-U09761-1 (Contig-U09761-1Q) /CSM_Contig/Conti...    36  0.027
Contig-U04714-1 (Contig-U04714-1Q) /CSM_Contig/Conti...    36  0.027
Contig-U14686-1 (Contig-U14686-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U14559-1 (Contig-U14559-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U14083-1 (Contig-U14083-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U12455-1 (Contig-U12455-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U12450-1 (Contig-U12450-1Q) /CSM_Contig/Conti...    34  0.11

>Contig-U07063-1 (Contig-U07063-1Q) /CSM_Contig/Contig-U07063-1Q.Seq.d
          Length = 396

 Score =  168 bits (85), Expect = 3e-42
 Identities = 115/130 (88%)
 Strand = Plus / Plus

                                                                       
Query: 1   ataaaaattaatatnnnnnnngcaacaacaacaatttgtatactaattggaattaaagat 60
           ||||||||||||||       |||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ataaaaattaatataaaaaaagcaacaacaacaatttgtatactaattggaattaaagat 60

                                                                       
Query: 61  taaatttacatgacaaggatggtgnnnnnnnnaatgaaaatagtaaatagtttcacaata 120
           ||||||||||||||||||||||||        ||||||||||||||||||||||||||||
Sbjct: 61  taaatttacatgacaaggatggtgttttttttaatgaaaatagtaaatagtttcacaata 120

                     
Query: 121 ttcacactca 130
           ||||||||||
Sbjct: 121 ttcacactca 130


 Score =  147 bits (74), Expect = 1e-35
 Identities = 88/95 (92%)
 Strand = Plus / Plus

                                                                       
Query: 184 attcaataaattgaaaaacatatatnnnnnnngtaataatatttttgtttttatcttttc 243
           |||||||||||||||||||||||||       ||||||||||||||||||||||||||||
Sbjct: 184 attcaataaattgaaaaacatatataaaaaaagtaataatatttttgtttttatcttttc 243

                                              
Query: 244 atatttaaacattgctaataacaatttcacatggg 278
           |||||||||||||||||||||||||||||||||||
Sbjct: 244 atatttaaacattgctaataacaatttcacatggg 278


 Score = 54.0 bits (27), Expect = 1e-07
 Identities = 33/33 (100%)
 Strand = Plus / Plus

                                            
Query: 315 cattttaattattattattgngnggtattgtct 347
           |||||||||||||||||||||||||||||||||
Sbjct: 315 cattttaattattattattgngnggtattgtct 347


>Contig-U14386-1 (Contig-U14386-1Q) /CSM_Contig/Contig-U14386-1Q.Seq.d
          Length = 509

 Score = 36.2 bits (18), Expect = 0.027
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 316 attttaattattattatt 333
           ||||||||||||||||||
Sbjct: 94  attttaattattattatt 77


>Contig-U11851-1 (Contig-U11851-1Q) /CSM_Contig/Contig-U11851-1Q.Seq.d
          Length = 1418

 Score = 36.2 bits (18), Expect = 0.027
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                              
Query: 316  attttaattattattatt 333
            ||||||||||||||||||
Sbjct: 1362 attttaattattattatt 1345


 Score = 28.2 bits (14), Expect = 6.6
 Identities = 17/18 (94%)
 Strand = Plus / Minus

                             
Query: 222 atatttttgtttttatct 239
           |||||| |||||||||||
Sbjct: 345 atatttatgtttttatct 328


  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: 24,045
Number of Sequences: 6905
Number of extensions: 24045
Number of successful extensions: 2607
Number of sequences better than 10.0: 718
length of query: 396
length of database: 5,674,871
effective HSP length: 16
effective length of query: 380
effective length of database: 5,564,391
effective search space: 2114468580
effective search space used: 2114468580
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 2008.11.11
Homology vs DNA 
Query= Contig-U07063-1 (Contig-U07063-1Q) /CSM_Contig/Contig-U07063-1Q.Seq.d
         (396 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

(AU270779) Dictyostelium discoideum vegetative cDNA clone:VS...   125   1e-64  5
(AU270780) Dictyostelium discoideum vegetative cDNA clone:VS...   125   8e-56  4
(EG612682) REPROTRACTF093614K4 POSSUM_01-POSSUM-C-REPROTRACT...    54   0.004  1
(EC364269) IMMUNEF093542B2 POSSUM_01-C-POSSUM-IMMUNE-2KB Tri...    54   0.004  1
(EC356721) LIVERF089486O14 POSSUM_01-POSSUM-LIVER-2KB Tricho...    54   0.004  1
(EX203370) SGT20w5_D02 normalized library from a mix of tamm...    54   0.004  1
(AC117070) Dictyostelium discoideum chromosome 2 map 2097701...    32   0.79   6
(CU459054) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   0.93   1
(AM450932) Vitis vinifera contig VV78X069306.7, whole genome...    38   1.9    2
(EF517791) Solanum melongena BAC 77N19, complete sequence.         34   2.8    6
(AC012595) Homo sapiens BAC clone RP11-539J22 from 2, comple...    40   3.0    2
(CU856449) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.7    1
(AM309376) Oryzias latipes EST, clone FOE002-P00036-DPE-F_K03.     44   3.7    1
(EY796321) CR05-C3-701-038-H10-CT.F Mandarin fruit, developm...    44   3.7    1
(AC154405) Mus musculus BAC clone RP24-248O10 from chromosom...    36   4.5    3
(AC212845) Populus trichocarpa clone POP021-P21, complete se...    36   9.2    3
(AC174185) Strongylocentrotus purpuratus clone R3-3044B5, WO...    42   9.9    3

>(AU270779) Dictyostelium discoideum vegetative cDNA clone:VSK189,
          5' end single read.
          Length = 397

 Score =  125 bits (63), Expect(5) = 1e-64
 Identities = 63/63 (100%)
 Strand = Plus / Plus


Query: 22 gcaacaacaacaatttgtatactaattggaattaaagattaaatttacatgacaaggatg 81
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 22 gcaacaacaacaatttgtatactaattggaattaaagattaaatttacatgacaaggatg 81


Query: 82 gtg 84
          |||
Sbjct: 82 gtg 84

 Score =  103 bits (52), Expect(5) = 1e-64
 Identities = 52/52 (100%)
 Strand = Plus / Plus


Query: 227 tttgtttttatcttttcatatttaaacattgctaataacaatttcacatggg 278
           ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 227 tttgtttttatcttttcatatttaaacattgctaataacaatttcacatggg 278

 Score = 50.1 bits (25), Expect(5) = 1e-64
 Identities = 31/31 (100%)
 Strand = Plus / Plus


Query: 317 ttttaattattattattgngnggtattgtct 347
           |||||||||||||||||||||||||||||||
Sbjct: 317 ttttaattattattattgngnggtattgtct 347

 Score = 36.2 bits (18), Expect(5) = 1e-64
 Identities = 18/18 (100%)
 Strand = Plus / Plus


Query: 93  aatgaaaatagtaaatag 110
           ||||||||||||||||||
Sbjct: 93  aatgaaaatagtaaatag 110

 Score = 28.2 bits (14), Expect(5) = 1e-64
 Identities = 14/14 (100%)
 Strand = Plus / Plus


Query: 1  ataaaaattaatat 14
          ||||||||||||||
Sbjct: 1  ataaaaattaatat 14

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 251,282,241
Number of extensions: 24766692
Number of successful extensions: 2109844
Number of sequences better than 10.0: 17
Length of query: 396
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 373
Effective length of database: 93,106,754,628
Effective search space: 34728819476244
Effective search space used: 34728819476244
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.23
Homology vs Protein 
Query= Contig-U07063-1 (Contig-U07063-1Q) /CSM_Contig/Contig-U07063-1Q.Seq.d
         (396 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 289,673,162
Number of extensions: 3455002
Number of successful extensions: 8242
Number of sequences better than 10.0: 0
Number of HSP's gapped: 8226
Number of HSP's successfully gapped: 0
Length of query: 132
Length of database: 1,040,966,779
Length adjustment: 97
Effective length of query: 35
Effective length of database: 730,151,134
Effective search space: 25555289690
Effective search space used: 25555289690
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: 29 (15.8 bits)
PSORT 

 psg: 0.45  gvh: 0.29  alm: 0.44  top: 0.53  tms: 0.00  mit: 0.30  mip: 0.00
 nuc: 0.12  erl: 0.00  erm: 0.40  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 %: nuclear
	 36.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: cytoskeletal

>> prediction for Contig-U07063-1 is nuc
VS (DIR, S) 1
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) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0