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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-U13097-1
Contig ID Contig-U13097-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13097-1 (Contig-U13097-1Q) /CSM_Contig/Contig-U13097-1Q.Seq.d
NNNNNNNNNNTGGTCAACAAGGNNTAANNCAANATTCAAATGGTTATTAT
ATTATTGGTAATAATACAAATCAATTAANANCAATCATNGGTAGATCAGT
NGCTGGTGATTCATCCTN
Gap no gap
Contig length 118
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 4588373
End point 4588481
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U13097
List of clone(s) 

est1=CHO387Z,1,109
Translated Amino Acid sequence 
XXXGQQGXXQXSNGYYIIGNNTNQLXXIXGRSVAGDSS
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxvnkx*xxiqmviillviiqin*xqsxvdqxlvihp


Frame B:
xxxwstrxxxxfkwllyyw**yksixxnhx*isxw*fil


Frame C:
XXXGQQGXXQXSNGYYIIGNNTNQLXXIXGRSVAGDSS
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13097-1 (Contig-U13097-1Q)
/CSM_Contig/Contig-U13097-1Q.Seq.d
         (118 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13097-1 (Contig-U13097-1Q) /CSM_Contig/Conti...   159  8e-40
Contig-U10748-1 (Contig-U10748-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U13854-1 (Contig-U13854-1Q) /CSM_Contig/Conti...    34  0.030
Contig-U08399-1 (Contig-U08399-1Q) /CSM_Contig/Conti...    34  0.030
Contig-U12818-1 (Contig-U12818-1Q) /CSM_Contig/Conti...    32  0.12
Contig-U09353-1 (Contig-U09353-1Q) /CSM_Contig/Conti...    32  0.12
Contig-U11548-1 (Contig-U11548-1Q) /CSM_Contig/Conti...    30  0.46
Contig-U10320-1 (Contig-U10320-1Q) /CSM_Contig/Conti...    30  0.46
Contig-U10301-1 (Contig-U10301-1Q) /CSM_Contig/Conti...    30  0.46
Contig-U02927-1 (Contig-U02927-1Q) /CSM_Contig/Conti...    30  0.46

>Contig-U13097-1 (Contig-U13097-1Q) /CSM_Contig/Contig-U13097-1Q.Seq.d
          Length = 118

 Score =  159 bits (80), Expect = 8e-40
 Identities = 107/107 (100%)
 Strand = Plus / Plus

                                                                       
Query: 11  tggtcaacaaggnntaanncaanattcaaatggttattatattattggtaataatacaaa 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11  tggtcaacaaggnntaanncaanattcaaatggttattatattattggtaataatacaaa 70

                                                          
Query: 71  tcaattaanancaatcatnggtagatcagtngctggtgattcatcct 117
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 71  tcaattaanancaatcatnggtagatcagtngctggtgattcatcct 117


>Contig-U10748-1 (Contig-U10748-1Q) /CSM_Contig/Contig-U10748-1Q.Seq.d
          Length = 4060

 Score = 36.2 bits (18), Expect = 0.007
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                              
Query: 54   attggtaataatacaaat 71
            ||||||||||||||||||
Sbjct: 1966 attggtaataatacaaat 1949


>Contig-U13854-1 (Contig-U13854-1Q) /CSM_Contig/Contig-U13854-1Q.Seq.d
          Length = 1319

 Score = 34.2 bits (17), Expect = 0.030
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                
Query: 52  ttattggtaataatacaaatc 72
           ||||||| |||||||||||||
Sbjct: 237 ttattggaaataatacaaatc 217


  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: 1761
Number of Sequences: 6905
Number of extensions: 1761
Number of successful extensions: 578
Number of sequences better than 10.0: 217
length of query: 118
length of database: 5,674,871
effective HSP length: 14
effective length of query: 104
effective length of database: 5,578,201
effective search space: 580132904
effective search space used: 580132904
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2008.12. 6
Homology vs DNA 
Query= Contig-U13097-1 (Contig-U13097-1Q) /CSM_Contig/Contig-U13097-1Q.Seq.d
         (118 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

(BJ384847) Dictyostelium discoideum cDNA clone:ddc50n21, 3' ...   159   2e-35  1
(AF287377) Barbus cyclolepis strumicae isolate Bstrum1556G A...    44   0.95   1
(AF287376) Barbus cyclolepis strumicae isolate Bstrum1555G A...    44   0.95   1
(AF287375) Barbus cyclolepis strumicae isolate Bcystru351G A...    44   0.95   1
(AC232014) Solanum tuberosum strain Diploid genotype RH89-03...    44   0.95   1
(DU927648) 351842 Tomato EcoRI BAC Library Solanum lycopersi...    40   1.3    2
(AC189479) Brassica rapa subsp. pekinensis clone KBrB081M20,...    42   3.7    1
(DJ386737) Diagnosis of Diseases Associated with Metastasis.       42   3.7    1
(AX349053) Sequence 511 from Patent WO0202807.                     42   3.7    1
(AX281533) Sequence 197 from Patent WO0177376.                     42   3.7    1
(AC068196) Homo sapiens BAC clone RP11-685J19 from 2, comple...    42   3.7    1
(AC127732) Rattus norvegicus clone CH230-407I1, *** SEQUENCI...    42   3.7    1
(AC099443) Rattus norvegicus clone CH230-197D1, *** SEQUENCI...    42   3.7    1
(CV109985) AGENCOURT_31531616 NIH_MGC_269 Rattus norvegicus ...    42   3.7    1
(BU028355) QHH12L01.yg.ab1 QH_EFGHJ sunflower RHA280 Heliant...    42   3.7    1
(AM662510) Entamoeba moshkovskii FIC GSS, clone mosh123e01.q1k.    34   5.1    2
(AC173043) Bos taurus clone CH240-98E10, WORKING DRAFT SEQUE...    30   6.8    2
(AC152094) Bos taurus clone CH240-2B20, WORKING DRAFT SEQUEN...    30   6.8    2
(AC167447) Bos taurus clone CH240-189K24, WORKING DRAFT SEQU...    30   7.0    2

>(BJ384847) Dictyostelium discoideum cDNA clone:ddc50n21, 3' end,
           single read.
          Length = 109

 Score =  159 bits (80), Expect = 2e-35
 Identities = 107/107 (100%)
 Strand = Plus / Minus


Query: 11  tggtcaacaaggnntaanncaanattcaaatggttattatattattggtaataatacaaa 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 109 tggtcaacaaggnntaanncaanattcaaatggttattatattattggtaataatacaaa 50


Query: 71  tcaattaanancaatcatnggtagatcagtngctggtgattcatcct 117
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 49  tcaattaanancaatcatnggtagatcagtngctggtgattcatcct 3

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 74,373,082
Number of extensions: 4941167
Number of successful extensions: 1274718
Number of sequences better than 10.0: 19
Length of query: 118
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 96
Effective length of database: 93,199,600,587
Effective search space: 8947161656352
Effective search space used: 8947161656352
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7. 5
Homology vs Protein 
Query= Contig-U13097-1 (Contig-U13097-1Q) /CSM_Contig/Contig-U13097-1Q.Seq.d
         (118 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 104,705,861
Number of extensions: 2571735
Number of successful extensions: 233
Number of sequences better than 10.0: 0
Number of HSP's gapped: 233
Number of HSP's successfully gapped: 0
Length of query: 39
Length of database: 1,051,180,864
Length adjustment: 13
Effective length of query: 26
Effective length of database: 1,009,105,597
Effective search space: 26236745522
Effective search space used: 26236745522
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: 24 (13.9 bits)
PSORT 

 psg: 0.78  gvh: 0.34  alm: 0.61  top: 0.53  tms: 0.00  mit: 0.23  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 

	 40.0 %: cytoplasmic
	 36.0 %: nuclear
	 12.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U13097-1 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) 0
CH (FL, L) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0