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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
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Contig-U06699-1
Contig ID Contig-U06699-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06699-1 (Contig-U06699-1Q) /CSM_Contig/Contig-U06699-1Q.Seq.d
CTAAAATCCTTAAGAATTGTACAATCTCTGATTTAAAATCAGTATCCTTA
GTTATTGAACAATTTAAATTACTATCAAACAAAACTAATCCATTAGAATA
TTTAAAAACTTCCTATCCATTAGTTTATCAACTCATCACTACTATACCTC
CTCAAACTCATCCTGGTTTTGAACCTCCAACTGAACGAGCTCTAGATTTT
TTAAATCGTCATTTAATTAATCCAACATCATCTGAAATTAAGATTTAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATNAAAAAAAA
Gap no gap
Contig length 298
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 5519119
End point 5518821
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U06699
List of clone(s) 

est1=VSF376F,1,299
est2=VSF376Z,1,184
Translated Amino Acid sequence 
KILKNCTISDLKSVSLVIEQFKLLSNKTNPLEYLKTSYPLVYQLITTIPPQTHPGFEPPT
ERALDFLNRHLINPTSSEIKI*kkkkkkkkkkkkkxkk
Translated Amino Acid sequence (All Frames) 
Frame A:
lkslrivqsli*nqyp*llnnlnyyqtklih*ni*klpih*finssllyllklilvlnlq
lnel*if*ivi*liqhhlklrfkkkkkkkkkkkkkkxkk


Frame B:
*np*elynl*fkisilsy*ti*itikqn*sirifknflsislsthhyytssnsswf*tsn
*tssrffkssfn*snii*n*dlkkkkkkkkkkkkknxkk


Frame C:
KILKNCTISDLKSVSLVIEQFKLLSNKTNPLEYLKTSYPLVYQLITTIPPQTHPGFEPPT
ERALDFLNRHLINPTSSEIKI*kkkkkkkkkkkkkxkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06699-1 (Contig-U06699-1Q)
/CSM_Contig/Contig-U06699-1Q.Seq.d
         (298 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06699-1 (Contig-U06699-1Q) /CSM_Contig/Conti...   488  e-138
Contig-U13627-1 (Contig-U13627-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U13611-1 (Contig-U13611-1Q) /CSM_Contig/Conti...    36  0.020
Contig-U14865-1 (Contig-U14865-1Q) /CSM_Contig/Conti...    34  0.080
Contig-U14190-1 (Contig-U14190-1Q) /CSM_Contig/Conti...    34  0.080
Contig-U13876-1 (Contig-U13876-1Q) /CSM_Contig/Conti...    34  0.080
Contig-U11781-1 (Contig-U11781-1Q) /CSM_Contig/Conti...    34  0.080
Contig-U11142-1 (Contig-U11142-1Q) /CSM_Contig/Conti...    34  0.080
Contig-U04624-1 (Contig-U04624-1Q) /CSM_Contig/Conti...    34  0.080
Contig-U13906-1 (Contig-U13906-1Q) /CSM_Contig/Conti...    32  0.32

>Contig-U06699-1 (Contig-U06699-1Q) /CSM_Contig/Contig-U06699-1Q.Seq.d
          Length = 298

 Score =  488 bits (246), Expect = e-138
 Identities = 246/246 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ctaaaatccttaagaattgtacaatctctgatttaaaatcagtatccttagttattgaac 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ctaaaatccttaagaattgtacaatctctgatttaaaatcagtatccttagttattgaac 60

                                                                       
Query: 61  aatttaaattactatcaaacaaaactaatccattagaatatttaaaaacttcctatccat 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aatttaaattactatcaaacaaaactaatccattagaatatttaaaaacttcctatccat 120

                                                                       
Query: 121 tagtttatcaactcatcactactatacctcctcaaactcatcctggttttgaacctccaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tagtttatcaactcatcactactatacctcctcaaactcatcctggttttgaacctccaa 180

                                                                       
Query: 181 ctgaacgagctctagattttttaaatcgtcatttaattaatccaacatcatctgaaatta 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ctgaacgagctctagattttttaaatcgtcatttaattaatccaacatcatctgaaatta 240

                 
Query: 241 agattt 246
           ||||||
Sbjct: 241 agattt 246


>Contig-U13627-1 (Contig-U13627-1Q) /CSM_Contig/Contig-U13627-1Q.Seq.d
          Length = 707

 Score = 40.1 bits (20), Expect = 0.001
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 54  attgaacaatttaaattact 73
           ||||||||||||||||||||
Sbjct: 182 attgaacaatttaaattact 201


>Contig-U13611-1 (Contig-U13611-1Q) /CSM_Contig/Contig-U13611-1Q.Seq.d
          Length = 639

 Score = 36.2 bits (18), Expect = 0.020
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 60  caatttaaattactatca 77
           ||||||||||||||||||
Sbjct: 618 caatttaaattactatca 601


  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: 3812
Number of Sequences: 6905
Number of extensions: 3812
Number of successful extensions: 1103
Number of sequences better than 10.0: 112
length of query: 298
length of database: 5,674,871
effective HSP length: 15
effective length of query: 283
effective length of database: 5,571,296
effective search space: 1576676768
effective search space used: 1576676768
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. 9
Homology vs DNA 
Query= Contig-U06699-1 (Contig-U06699-1Q) /CSM_Contig/Contig-U06699-1Q.Seq.d
         (298 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

(AC116960) Dictyostelium discoideum chromosome 2 map complem...   488   e-134  1
(AU265137) Dictyostelium discoideum vegetative cDNA clone:VS...   488   e-134  1
(AU265138) Dictyostelium discoideum vegetative cDNA clone:VS...   347   1e-91  1
(ED926150) OA_CBa0100B21.r OA_CBa Oryza australiensis genomi...    46   0.69   1
(ED851795) OA_CBa0020M04.r OA_CBa Oryza australiensis genomi...    46   0.69   1
(ED849946) OA_CBa0018F13.f OA_CBa Oryza australiensis genomi...    46   0.69   1
(CL914306) OA_ABa0016B03.r OA_ABa Oryza australiensis genomi...    46   0.69   1
(AE014266) Streptococcus agalactiae 2603V/R section 76 of 10...    38   1.1    2
(AX602195) Sequence 124 from Patent WO02092818.                    38   1.9    2
(BV637244) S217P60654RA7.T0 Noemie Pan troglodytes troglodyt...    44   2.7    1
(AM483679) Vitis vinifera contig VV78X174607.9, whole genome...    44   2.7    1
(AC090530) Homo sapiens chromosome 1 clone RP11-416G1, compl...    44   2.7    1
(EK344382) 1095467196827 Global-Ocean-Sampling_GS-31-01-01-1...    44   2.7    1
(Z97601) Rhainopomma montanum mitochondrial 12S rRNA gene (p...    38   3.9    2
(AL766852) Streptococcus agalactiae NEM316 complete genome, ...    38   6.3    2
(AB016888) Arabidopsis thaliana genomic DNA, chromosome 5, P...    34   8.6    4
(EH779510) CNSS18344.b1_P02.ab1 CNS(LMS) yellow starthistle ...    38   8.8    2
(ER629630) 1093018408575 Global-Ocean-Sampling_GS-36-01-01-2...    36   9.3    2
(CR848040) Zebrafish DNA sequence from clone DKEY-19P15 in l...    34   9.8    4

>(AC116960) Dictyostelium discoideum chromosome 2 map
             complement(1004496-821614) strain AX4, complete sequence.
          Length = 182870

 Score =  488 bits (246), Expect = e-134
 Identities = 246/246 (100%)
 Strand = Plus / Minus


Query: 1     ctaaaatccttaagaattgtacaatctctgatttaaaatcagtatccttagttattgaac 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42974 ctaaaatccttaagaattgtacaatctctgatttaaaatcagtatccttagttattgaac 42915


Query: 61    aatttaaattactatcaaacaaaactaatccattagaatatttaaaaacttcctatccat 120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42914 aatttaaattactatcaaacaaaactaatccattagaatatttaaaaacttcctatccat 42855


Query: 121   tagtttatcaactcatcactactatacctcctcaaactcatcctggttttgaacctccaa 180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42854 tagtttatcaactcatcactactatacctcctcaaactcatcctggttttgaacctccaa 42795


Query: 181   ctgaacgagctctagattttttaaatcgtcatttaattaatccaacatcatctgaaatta 240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42794 ctgaacgagctctagattttttaaatcgtcatttaattaatccaacatcatctgaaatta 42735


Query: 241   agattt 246
             ||||||
Sbjct: 42734 agattt 42729

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 325,928,807
Number of extensions: 19734164
Number of successful extensions: 1477084
Number of sequences better than 10.0: 19
Length of query: 298
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 275
Effective length of database: 93,106,754,628
Effective search space: 25604357522700
Effective search space used: 25604357522700
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06699-1 (Contig-U06699-1Q) /CSM_Contig/Contig-U06699-1Q.Seq.d
         (298 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116960_22(AC116960|pid:none) Dictyostelium discoideum chromoso...   160   2e-38
CP000499_173(CP000499|pid:none) Pichia stipitis CBS 6054 chromos...    33   2.3
CP000875_514(CP000875|pid:none) Herpetosiphon aurantiacus ATCC 2...    32   8.9

>AC116960_22(AC116960|pid:none) Dictyostelium discoideum chromosome 2
            map complement(1004496-821614) strain AX4, complete
            sequence.
          Length = 1163

 Score =  160 bits (404), Expect = 2e-38
 Identities = 78/78 (100%), Positives = 78/78 (100%)
 Frame = +3

Query: 3    KILKNCTISDLKSVSLVIEQFKLLSNKTNPLEYLKTSYPLVYQLITTIPPQTHPGFEPPT 182
            KILKNCTISDLKSVSLVIEQFKLLSNKTNPLEYLKTSYPLVYQLITTIPPQTHPGFEPPT
Sbjct: 1083 KILKNCTISDLKSVSLVIEQFKLLSNKTNPLEYLKTSYPLVYQLITTIPPQTHPGFEPPT 1142

Query: 183  ERALDFLNRHLINPTSSE 236
            ERALDFLNRHLINPTSSE
Sbjct: 1143 ERALDFLNRHLINPTSSE 1160

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: 233,819,548
Number of extensions: 2931835
Number of successful extensions: 11623
Number of sequences better than 10.0: 3
Number of HSP's gapped: 11621
Number of HSP's successfully gapped: 3
Length of query: 99
Length of database: 1,040,966,779
Length adjustment: 68
Effective length of query: 31
Effective length of database: 823,075,399
Effective search space: 25515337369
Effective search space used: 25515337369
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: 0.82  gvh: 0.40  alm: 0.44  top: 0.53  tms: 0.00  mit: 0.29  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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 

	 36.0 %: nuclear
	 28.0 %: cytoplasmic
	 24.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U06699-1 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