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Dicty_cDB
Contig List | Clone List | cDNA Library List
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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-U04579-1
Contig ID Contig-U04579-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U04579-1 (Contig-U04579-1Q) /CSM_Contig/Contig-U04579-1Q.Seq.d
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAACAGTGTGGTTTTTTTTTAAATAAATATTATTTATTTGTT
GTTGTATTTTATAATTATTTATTTATTATATTTTTTGTAATATTAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAGAAAATAAAAAATCAAAAAAAATCAA
AAAAAGAAAAATCGAATAATACATTAATATCTTTTAATTTTAATATATTT
TCGAAAAAAAGGAAAAAAAAATAAAAAAAGCAATAAATAAGAAATAAGGA
ATAAG
Gap no gap
Contig length 305
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 2399015
End point 2398789
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U04579
List of clone(s) 

est1=SSB586Z,1,306
Translated Amino Acid sequence 
KKKKKKKKKKKKKKKKKKKKQCGFFLNKYYLFVVVFYNYLFIIFFVILKKKKKKKKKKKI
KNQKKSKKEKSNNTLISFNFNIFSKKRKKK*kkq*irnke*
Translated Amino Acid sequence (All Frames) 
Frame A:
kkkkkkkkkkkkkkkkkkkktvwfffk*ilficccil*lfiyyifcnikkkkkkkkkken
kkskkikkrkie*yinif*f*yifekkekkikkainkk*gi


Frame B:
KKKKKKKKKKKKKKKKKKKKQCGFFLNKYYLFVVVFYNYLFIIFFVILKKKKKKKKKKKI
KNQKKSKKEKSNNTLISFNFNIFSKKRKKK*kkq*irnke*


Frame C:
kkkkkkkkkkkkkkkkkkknsvvff*iniiylllyfiiiyllyfl*y*kkkkkkkkkrk*
kikknqkkknriih*ylliliyfrkkgkknkksnk*eirnk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04579-1 (Contig-U04579-1Q)
/CSM_Contig/Contig-U04579-1Q.Seq.d
         (305 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04579-1 (Contig-U04579-1Q) /CSM_Contig/Conti...    84  1e-16
Contig-U12098-1 (Contig-U12098-1Q) /CSM_Contig/Conti...    38  0.005
Contig-U06545-1 (Contig-U06545-1Q) /CSM_Contig/Conti...    38  0.005
Contig-U05732-1 (Contig-U05732-1Q) /CSM_Contig/Conti...    38  0.005
Contig-U12509-1 (Contig-U12509-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U06097-1 (Contig-U06097-1Q) /CSM_Contig/Conti...    34  0.082
Contig-U04769-1 (Contig-U04769-1Q) /CSM_Contig/Conti...    34  0.082
Contig-U01973-1 (Contig-U01973-1Q) /CSM_Contig/Conti...    34  0.082
Contig-U01957-1 (Contig-U01957-1Q) /CSM_Contig/Conti...    34  0.082
Contig-U14394-1 (Contig-U14394-1Q) /CSM_Contig/Conti...    32  0.33

>Contig-U04579-1 (Contig-U04579-1Q) /CSM_Contig/Contig-U04579-1Q.Seq.d
          Length = 305

 Score = 83.8 bits (42), Expect = 1e-16
 Identities = 42/42 (100%)
 Strand = Plus / Plus

                                                     
Query: 212 tcgaataatacattaatatcttttaattttaatatattttcg 253
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 212 tcgaataatacattaatatcttttaattttaatatattttcg 253


 Score = 52.0 bits (26), Expect = 4e-07
 Identities = 26/26 (100%)
 Strand = Plus / Plus

                                     
Query: 280 gcaataaataagaaataaggaataag 305
           ||||||||||||||||||||||||||
Sbjct: 280 gcaataaataagaaataaggaataag 305


>Contig-U12098-1 (Contig-U12098-1Q) /CSM_Contig/Contig-U12098-1Q.Seq.d
          Length = 723

 Score = 38.2 bits (19), Expect = 0.005
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                              
Query: 232 ttttaattttaatatattt 250
           |||||||||||||||||||
Sbjct: 112 ttttaattttaatatattt 94


>Contig-U06545-1 (Contig-U06545-1Q) /CSM_Contig/Contig-U06545-1Q.Seq.d
          Length = 566

 Score = 38.2 bits (19), Expect = 0.005
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                              
Query: 224 ttaatatcttttaatttta 242
           |||||||||||||||||||
Sbjct: 231 ttaatatcttttaatttta 213


  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: 2522
Number of Sequences: 6905
Number of extensions: 2522
Number of successful extensions: 1024
Number of sequences better than 10.0: 129
length of query: 305
length of database: 5,674,871
effective HSP length: 15
effective length of query: 290
effective length of database: 5,571,296
effective search space: 1615675840
effective search space used: 1615675840
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. 6.25
Homology vs DNA 
Query= Contig-U04579-1 (Contig-U04579-1Q) /CSM_Contig/Contig-U04579-1Q.Seq.d
         (305 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

(AU037189) Dictyostelium discoideum slug cDNA, clone SSB586.       84   6e-22  2
(DU054594) 92238 Tomato HindIII BAC Library Solanum lycopers...    50   0.048  1
(AC169395) Macaca mulatta clone CH250-10M4, WORKING DRAFT SE...    48   0.19   1
(EJ114233) 1092343258425 Global-Ocean-Sampling_GS-27-01-01-1...    48   0.19   1
(CZ499571) GMW2-21E7a.g1 GMW2 Glycine max genomic, genomic s...    48   0.19   1
(AG653499) Macaca fuscata fuscata DNA, clone: MSB2-069I08_R,...    48   0.19   1
(AL954861) Zebrafish DNA sequence from clone CH211-8I17.           34   0.42   2
(CU019625) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    34   0.42   2
(AC094417) Rattus norvegicus clone CH230-3N8, WORKING DRAFT ...    46   0.75   1
(FI266530) CccaBb034-P16JR CccABb Cajanus cajan genomic clon...    46   0.75   1
(FI252525) CccaBb017-J13JR CccABb Cajanus cajan genomic clon...    46   0.75   1
(FI072106) CHO_OF7325xd20f1.ab1 CHO_OF7 Nicotiana tabacum ge...    46   0.75   1
(FH732037) CHO_OF5113xo12r1.ab1 CHO_OF5 Nicotiana tabacum ge...    46   0.75   1
(FH695611) CHO_OF5128xn17r1.ab1 CHO_OF5 Nicotiana tabacum ge...    46   0.75   1
(ET787452) CHO_OF638xp01r1.ab1 CHO_OF Nicotiana tabacum geno...    46   0.75   1
(ET750320) CHO_OF304xj09r1.ab1 CHO_OF Nicotiana tabacum geno...    46   0.75   1
(DH782200) Rattus norvegicus DNA, BAC clone: RNB1-370P03, 5'...    46   0.75   1
(CT014370) KBrH122M12 genomic clone, KBrH (HindIII) BAC libr...    46   0.75   1
(FK189328) XABT204277.g1 Gateway compatible cien cDNA librar...    40   2.3    2
(CT574587) Zebrafish DNA sequence from clone CH211-80N22 in ...    44   3.0    1
(BX957337) Zebrafish DNA sequence from clone DKEY-211E8 in l...    44   3.0    1
(AC189502) Brassica rapa subsp. pekinensis clone KBrB087M20,...    44   3.0    1
(AC004253) Homo sapiens chromosome 17, clone CTC-542B22, com...    44   3.0    1
(AC148286) Rhinolophus ferrumequinum clone VMRC7-266I21, WOR...    44   3.0    1
(AC106527) Rattus norvegicus clone CH230-26E17, *** SEQUENCI...    44   3.0    1
(AC212074) Pongo abelii chromosome UNKNOWN clone CH276-284G5...    44   3.0    1
(FI314523) AdH1170-CPY2-M23TF AdH1 Arachis duranensis genomi...    44   3.0    1
(FH419709) CHO_OF4887xd14r1.ab1 CHO_OF4 Nicotiana tabacum ge...    44   3.0    1
(EK025769) 1092955365702 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.0    1
(ED461689) AUAC-aaq41a05.g1 Ascaris suum whole genome shotgu...    44   3.0    1
(DU948437) 229926 Tomato MboI BAC Library Solanum lycopersic...    44   3.0    1
(DU029543) 10581 Tomato HindIII BAC Library Solanum lycopers...    44   3.0    1
(DU026489) 7121 Tomato HindIII BAC Library Solanum lycopersi...    44   3.0    1
(DH600812) Rattus norvegicus DNA, BAC clone: RNB1-126K06, 3'...    44   3.0    1
(CT533242) A BAC library has been constructed from cultivar ...    44   3.0    1
(EC272152) TT1BT61TV Tetrahymena thermophila SB210 cDNA libr...    44   3.0    1
(CP001056) Clostridium botulinum B str. Eklund 17B, complete...    44   3.0    1
(AM285305) Spiroplasma citri GII3-3X chromosome, contig Cont...    44   3.0    1
(BX901877) Zebrafish DNA sequence from clone CH211-173P17 in...    38   4.5    2
(EU124739) Solanum lycopersicum chromosome 3 clone C03HBa023...    42   4.7    3
(AP001967) Homo sapiens genomic DNA, chromosome 4q22-q24, cl...    42   5.1    2
(CU929051) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    38   5.3    2
(AC176849) Strongylocentrotus purpuratus clone R3-1110I17, W...    32   5.6    2
(AC104059) Homo sapiens BAC clone RP13-514E23 from 4, comple...    42   6.7    2
(AC012208) Homo sapiens chromosome 4 clone RP11-375K17 map 4...    42   7.1    2
(AC162243) Bos taurus clone CH240-111K18, WORKING DRAFT SEQU...    40   7.2    2
(AY809785) Schistosoma japonicum SJCHGC05575 protein mRNA, p...    30   7.3    2
(ER523211) 1093015602388 Global-Ocean-Sampling_GS-35-01-01-1...    32   7.4    2
(ED716906) GM_WBb0066O12.f GM_WBb Glycine max genomic clone ...    32   7.5    2
(FH373596) CHO_OF4574xi02f1.ab1 CHO_OF4 Nicotiana tabacum ge...    30   7.5    2
(CV746397) SJL_31_004__1-3__15.T3_020.ab1 SJL Schistosoma ja...    30   7.5    2
(BH980407) ode81a08.b1 B.oleracea002 Brassica oleracea genom...    30   7.5    2
(BH695148) BOMEY25TR BO_2_3_KB Brassica oleracea genomic clo...    30   7.6    2
(ED694515) GM_WBb0033D18.r GM_WBb Glycine max genomic clone ...    38   8.5    2

>(AU037189) Dictyostelium discoideum slug cDNA, clone SSB586.
          Length = 306

 Score = 83.8 bits (42), Expect(2) = 6e-22
 Identities = 42/42 (100%)
 Strand = Plus / Plus


Query: 212 tcgaataatacattaatatcttttaattttaatatattttcg 253
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 212 tcgaataatacattaatatcttttaattttaatatattttcg 253

 Score = 52.0 bits (26), Expect(2) = 6e-22
 Identities = 26/26 (100%)
 Strand = Plus / Plus


Query: 280 gcaataaataagaaataaggaataag 305
           ||||||||||||||||||||||||||
Sbjct: 280 gcaataaataagaaataaggaataag 305

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 123,788,486
Number of extensions: 9814747
Number of successful extensions: 1154107
Number of sequences better than 10.0: 56
Length of query: 305
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 282
Effective length of database: 99,442,330,388
Effective search space: 28042737169416
Effective search space used: 28042737169416
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04579-1 (Contig-U04579-1Q) /CSM_Contig/Contig-U04579-1Q.Seq.d
         (305 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: 49,315,427
Number of extensions: 108449
Number of successful extensions: 42
Number of sequences better than 10.0: 0
Number of HSP's gapped: 42
Number of HSP's successfully gapped: 0
Length of query: 101
Length of database: 1,061,185,681
Length adjustment: 69
Effective length of query: 32
Effective length of database: 835,662,769
Effective search space: 26741208608
Effective search space used: 26741208608
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: 0.03  gvh: 0.25  alm: 0.18  top: 0.80  tms: 0.07  mit: 0.25  mip: 0.00
 nuc: 2.47  erl: 0.00  erm: 1.00  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  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: 1.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 44.0 %: nuclear
	 16.0 %: mitochondrial
	 12.0 %: cytoplasmic
	  8.0 %: plasma membrane
	  8.0 %: endoplasmic reticulum
	  4.0 %: Golgi
	  4.0 %: vesicles of secretory system
	  4.0 %: peroxisomal

>> prediction for Contig-U04579-1 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