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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-U06239-1
Contig ID Contig-U06239-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06239-1 (Contig-U06239-1Q) /CSM_Contig/Contig-U06239-1Q.Seq.d
ACAAGATGTTGGTGTGTTTTCACCATCATTAAAAATGTTTATGAAATGTG
GAAGACTAACAAAAGAGGGATTCATATTCCAAAATCCTGAAAATAATTGC
CCAATTCATGATGATTTTAAAAAATCAAATACAATTATTAAATCAATCAC
TGAAAAGGTTAATAATTCATTATTACTCTTTTTATTTGGAAACAAAGAAG
AAAATCCAACTACTTCACATGAAGGATCTCCATTACCCACTAGTGAAAAT
ACTCTTGATAAAAATAATAATAATAATAATAATAAAGATTAATTTTTAAA
TAAATTTATTTTTGTGTTAATTTAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 371
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 994386
End point 994061
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U06239
List of clone(s) 

est1=VSA321Z,1,372
Translated Amino Acid sequence 
QDVGVFSPSLKMFMKCGRLTKEGFIFQNPENNCPIHDDFKKSNTIIKSITEKVNNSLLLF
LFGNKEENPTTSHEGSPLPTSENTLDKNNNNNNNKD*flnkfifvli*kkkkkkkkkkkk
kkk
Translated Amino Acid sequence (All Frames) 
Frame A:
trcwcvftiiknvyemwktnkrgihipks*k*lpns**f*kikyny*inh*kg**fiitl
fiwkqrrksnyft*risith**kys**k*******rlifk*iyfcvnlkkkkkkkkkkkk
kkk


Frame B:
QDVGVFSPSLKMFMKCGRLTKEGFIFQNPENNCPIHDDFKKSNTIIKSITEKVNNSLLLF
LFGNKEENPTTSHEGSPLPTSENTLDKNNNNNNNKD*flnkfifvli*kkkkkkkkkkkk
kkk


Frame C:
kmlvcfhhh*kcl*nved*qkrdsyskilkiiaqfmmilknqiqllnqslkrliihyysf
yletkkkiqllhmkdlhyplvkillikiiiiiiikinf*inlflc*fkkkkkkkkkkkkk
kkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06239-1 (Contig-U06239-1Q)
/CSM_Contig/Contig-U06239-1Q.Seq.d
         (371 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06239-1 (Contig-U06239-1Q) /CSM_Contig/Conti...   507  e-144
Contig-U14818-1 (Contig-U14818-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U14770-1 (Contig-U14770-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U14741-1 (Contig-U14741-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U04283-1 (Contig-U04283-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U13498-1 (Contig-U13498-1Q) /CSM_Contig/Conti...    36  0.025
Contig-U12316-1 (Contig-U12316-1Q) /CSM_Contig/Conti...    36  0.025
Contig-U11587-1 (Contig-U11587-1Q) /CSM_Contig/Conti...    36  0.025
Contig-U11404-1 (Contig-U11404-1Q) /CSM_Contig/Conti...    36  0.025

>Contig-U06239-1 (Contig-U06239-1Q) /CSM_Contig/Contig-U06239-1Q.Seq.d
          Length = 371

 Score =  507 bits (256), Expect = e-144
 Identities = 256/256 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   acaagatgttggtgtgttttcaccatcattaaaaatgtttatgaaatgtggaagactaac 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   acaagatgttggtgtgttttcaccatcattaaaaatgtttatgaaatgtggaagactaac 60

                                                                       
Query: 61  aaaagagggattcatattccaaaatcctgaaaataattgcccaattcatgatgattttaa 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aaaagagggattcatattccaaaatcctgaaaataattgcccaattcatgatgattttaa 120

                                                                       
Query: 121 aaaatcaaatacaattattaaatcaatcactgaaaaggttaataattcattattactctt 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 aaaatcaaatacaattattaaatcaatcactgaaaaggttaataattcattattactctt 180

                                                                       
Query: 181 tttatttggaaacaaagaagaaaatccaactacttcacatgaaggatctccattacccac 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tttatttggaaacaaagaagaaaatccaactacttcacatgaaggatctccattacccac 240

                           
Query: 241 tagtgaaaatactctt 256
           ||||||||||||||||
Sbjct: 241 tagtgaaaatactctt 256


 Score = 36.2 bits (18), Expect = 0.025
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 306 ttatttttgtgttaattt 323
           ||||||||||||||||||
Sbjct: 306 ttatttttgtgttaattt 323


>Contig-U14818-1 (Contig-U14818-1Q) /CSM_Contig/Contig-U14818-1Q.Seq.d
          Length = 819

 Score = 40.1 bits (20), Expect = 0.002
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 117 ttaaaaaatcaaatacaatt 136
           ||||||||||||||||||||
Sbjct: 630 ttaaaaaatcaaatacaatt 649


>Contig-U14770-1 (Contig-U14770-1Q) /CSM_Contig/Contig-U14770-1Q.Seq.d
          Length = 614

 Score = 38.2 bits (19), Expect = 0.006
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                  
Query: 123 aatcaaatacaattattaaatca 145
           ||||||| |||||||||||||||
Sbjct: 3   aatcaaaaacaattattaaatca 25


  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: 6536
Number of Sequences: 6905
Number of extensions: 6536
Number of successful extensions: 703
Number of sequences better than 10.0: 256
length of query: 371
length of database: 5,674,871
effective HSP length: 16
effective length of query: 355
effective length of database: 5,564,391
effective search space: 1975358805
effective search space used: 1975358805
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. 7
Homology vs DNA 
Query= Contig-U06239-1 (Contig-U06239-1Q) /CSM_Contig/Contig-U06239-1Q.Seq.d
         (371 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

(AU261419) Dictyostelium discoideum vegetative cDNA clone:VS...   509   e-140  1
(AU074484) Dictyostelium discoideum slug cDNA, clone SSK874.      103   4e-18  1
(AC128724) Rattus norvegicus clone CH230-181K6, WORKING DRAF...    34   0.13   2
(AC114223) Rattus norvegicus clone CH230-320K6, *** SEQUENCI...    34   0.13   2
(AC093184) Rattus norvegicus strain Brown Norway clone RP31-...    34   0.13   2
(CT748491) Paramecium tetraurelia 5-PRIME EST from clone LK0...    36   0.17   2
(DH094859) Oryzias latipes Fosmid clone:GOLWFno151_c23, reve...    48   0.22   1
(EV848875) TT1EX09TV Tetrahymena thermophila SB210 cDNA libr...    36   0.61   2
(EJ767788) 1092963324930 Global-Ocean-Sampling_GS-30-02-01-1...    34   0.62   2
(EV848874) TT1EX09TH Tetrahymena thermophila SB210 cDNA libr...    36   0.62   2
(EV837978) FMMA037TF Tetrahymena thermophila SB210 cDNA libr...    36   0.62   2
(CX586962) TTE00021386 Amplicon Express - Conjugative Form T...    36   0.62   2
(EJ758654) 1092963105494 Global-Ocean-Sampling_GS-30-02-01-1...    34   0.62   2
(EJ291070) 1095383001695 Global-Ocean-Sampling_GS-27-01-01-1...    34   0.62   2
(CU104777) Zebrafish DNA sequence from clone CH1073-172F18 i...    46   0.87   1
(AM480406) Vitis vinifera, whole genome shotgun sequence, co...    46   0.87   1
(DX534263) GH_MBb0021C13f GH_MBb Gossypium hirsutum genomic ...    46   0.87   1
(CT606127) Danio rerio EST, clone ZF_mu_183h08 3'.                 46   0.87   1
(CK402471) AUF_IfInt_206_f09 Ictalurus furcatus intestine cD...    46   0.87   1
(AC167913) Bos taurus clone CH240-196M16, WORKING DRAFT SEQU...    36   0.89   4
(AC214629) Populus trichocarpa clone POP050-E16, complete se...    44   1.3    4
(DQ343646) Trypanosoma cruzi strain Esmeraldo kinetoplast ma...    40   1.6    2
(CU915803) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    34   1.8    2
(EK252472) 1095460286329 Global-Ocean-Sampling_GS-31-01-01-1...    34   2.3    2
(BX087955) AGENAE Rainbow trout multi-tissues - normalized +...    32   2.3    2
(CT326383) Sus scrofa genomic clone CH242-310C21, genomic su...    34   2.3    2
(CZ118068) OA_BBa0003P06.f OA_BBa Oryza alta genomic clone O...    34   2.4    2
(AC107381) Homo sapiens BAC clone RP11-41F9 from 4, complete...    36   2.4    3
(AC214279) Populus trichocarpa clone ACSB1385-N19, complete ...    42   2.5    2
(BX855598) Zebrafish DNA sequence from clone DKEY-52J13 in l...    44   3.4    1
(AP008216) Oryza sativa (japonica cultivar-group) genomic DN...    44   3.4    1
(AC092389) Oryza sativa chromosome 10 BAC OSJNBa0053C23 geno...    44   3.4    1
(AL954650) Human DNA sequence from clone RP11-523M19 on chro...    44   3.4    1
(AC087258) Homo sapiens 12p BAC RP11-686N4 (Roswell Park Can...    44   3.4    1
(AC160662) Bos taurus clone CH240-96L13, WORKING DRAFT SEQUE...    44   3.4    1
(AC122598) Rattus norvegicus clone CH230-61D24, *** SEQUENCI...    44   3.4    1
(AC096323) Rattus norvegicus clone CH230-61D23, *** SEQUENCI...    44   3.4    1
(CU606934) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.4    1
(AC076960) Homo sapiens chromosome 3 clone RP11-135D21, WORK...    44   3.4    1
(AC220639) Bos taurus clone CH240-351H11, WORKING DRAFT SEQU...    44   3.4    1
(AC208123) Zea mays chromosome 1 clone CH201-507F10; ZMMBBc0...    44   3.4    1
(AC180787) Strongylocentrotus purpuratus clone R3-3072A21, W...    44   3.4    1
(FH490000) CHO_OF4519xa10r1.ab1 CHO_OF4 Nicotiana tabacum ge...    44   3.4    1
(ET887001) CHO_OF433xa22r1.ab1 CHO_OF Nicotiana tabacum geno...    44   3.4    1
(EK200850) 1095460056092 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.4    1
(EJ379808) 1092963757068 Global-Ocean-Sampling_GS-28-01-01-1...    44   3.4    1
(EJ102771) 1091140850083 Global-Ocean-Sampling_GS-27-01-01-1...    44   3.4    1
(CR340787) mte1-72J2RM1 BAC end, cultivar Jemalong A17 of Me...    44   3.4    1
(CL648650) CH213-189H20.T7 CH213 Gasterosteus aculeatus geno...    44   3.4    1
(CG346002) OGVDW18TV ZM_0.7_1.5_KB Zea mays genomic clone ZM...    44   3.4    1
(BZ372650) ie70b09.b1 WGS-ZmaysF (DH5a methyl filtered) Zea ...    44   3.4    1
(EH365917) e06_j001_plate_59 j001 Nicotiana benthamiana cDNA...    44   3.4    1
(EH365825) g04_j001_plate_57 j001 Nicotiana benthamiana cDNA...    44   3.4    1
(FD457408) EGGBD75TF Haematobia irritans eggs Haematobia irr...    44   3.4    1
(AE016830) Enterococcus faecalis V583, complete genome.            44   3.4    1
(AC159501) Bos taurus clone CH240-71M20, WORKING DRAFT SEQUE...    36   4.0    4
(AC220277) Bos taurus clone CH240-368F15, WORKING DRAFT SEQU...    38   4.1    3
(AC113010) Mus musculus chromosome 18, clone RP23-172F6, com...    32   6.2    2
(CZ788852) OC__Ba0153G02.f OC__Ba Oryza coarctata genomic cl...    36   6.9    2
(BX649415) Zebrafish DNA sequence from clone RP71-84D9 in li...    38   7.0    2
(AC222242) Bos taurus clone CH240-413B1, WORKING DRAFT SEQUE...    36   7.1    4
(AM454450) Vitis vinifera contig VV78X074213.4, whole genome...    42   7.2    2
(AF486073) Acute bee paralysis virus isolate Poland 1, compl...    32   7.5    2
(AC146310) Oryza sativa Japonica Group chromosome 10 clone B...    38   7.9    2
(AG320830) Mus musculus molossinus DNA, clone:MSMg01-106N17....    32   8.4    2
(AY053376) Acute bee paralysis virus isolate Poland 4 capsid...    32   8.7    2
(AF264692) Acute bee paralysis virus isolate ballapv12 struc...    32   8.8    2
(AF264691) Acute bee paralysis virus isolate ballapv8 struct...    32   8.8    2
(AF264690) Acute bee paralysis virus isolate ballapv7 struct...    32   8.8    2
(AF264689) Acute bee paralysis virus isolate ballapv6 struct...    32   8.8    2
(AF264688) Acute bee paralysis virus isolate ballapv5 struct...    32   8.8    2
(AF263736) Acute bee paralysis virus isolate 950411b-6 struc...    32   8.8    2
(AF263735) Acute bee paralysis virus isolate 950411b-5 struc...    32   8.8    2
(AF263734) Acute bee paralysis virus isolate 950411b-4 struc...    32   8.8    2
(AF263733) Acute bee paralysis virus isolate 950411b-2 struc...    32   8.8    2
(AF263724) Acute bee paralysis virus isolate 950404c-2 struc...    32   8.8    2

>(AU261419) Dictyostelium discoideum vegetative cDNA clone:VSA321,
           3' end single read.
          Length = 372

 Score =  509 bits (257), Expect = e-140
 Identities = 257/257 (100%)
 Strand = Plus / Plus


Query: 1   acaagatgttggtgtgttttcaccatcattaaaaatgtttatgaaatgtggaagactaac 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   acaagatgttggtgtgttttcaccatcattaaaaatgtttatgaaatgtggaagactaac 60


Query: 61  aaaagagggattcatattccaaaatcctgaaaataattgcccaattcatgatgattttaa 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aaaagagggattcatattccaaaatcctgaaaataattgcccaattcatgatgattttaa 120


Query: 121 aaaatcaaatacaattattaaatcaatcactgaaaaggttaataattcattattactctt 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 aaaatcaaatacaattattaaatcaatcactgaaaaggttaataattcattattactctt 180


Query: 181 tttatttggaaacaaagaagaaaatccaactacttcacatgaaggatctccattacccac 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tttatttggaaacaaagaagaaaatccaactacttcacatgaaggatctccattacccac 240


Query: 241 tagtgaaaatactcttg 257
           |||||||||||||||||
Sbjct: 241 tagtgaaaatactcttg 257

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 423,375,883
Number of extensions: 29067889
Number of successful extensions: 2466231
Number of sequences better than 10.0: 77
Length of query: 371
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 348
Effective length of database: 93,106,754,628
Effective search space: 32401150610544
Effective search space used: 32401150610544
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.21
Homology vs Protein 
Query= Contig-U06239-1 (Contig-U06239-1Q) /CSM_Contig/Contig-U06239-1Q.Seq.d
         (371 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP000742_972(CP000742|pid:none) Methanococcus vannielii SB, comp...    37   0.28
AE000511_449(AE000511|pid:none) Helicobacter pylori 26695, compl...    34   1.8
AE016830_1420(AE016830|pid:none) Enterococcus faecalis V583, com...    33   2.4
CP001217_975(CP001217|pid:none) Helicobacter pylori P12, complet...    33   4.0
CP000282_1593(CP000282|pid:none) Saccharophagus degradans 2-40, ...    32   6.8

>CP000742_972(CP000742|pid:none) Methanococcus vannielii SB,
           complete genome.
          Length = 226

 Score = 36.6 bits (83), Expect = 0.28
 Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
 Frame = +2

Query: 50  GRLTKEGFIFQNPENNCPIHDDFKKSNTIIKSITEKVNNSLLLFLF-GNKEENPT 211
           G  TK  F+  N ENN    DDF K N  +    + +NNS+ +FL  GN ++  T
Sbjct: 31  GDFTKHSFVKNNQENN---QDDFFKKNLKLLEFLKNLNNSVKIFLIPGNWDDKET 82

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: 468,715,262
Number of extensions: 7884593
Number of successful extensions: 19654
Number of sequences better than 10.0: 5
Number of HSP's gapped: 19654
Number of HSP's successfully gapped: 5
Length of query: 123
Length of database: 1,040,966,779
Length adjustment: 89
Effective length of query: 34
Effective length of database: 755,785,414
Effective search space: 25696704076
Effective search space used: 25696704076
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: 0.70  gvh: 0.20  alm: 0.46  top: 0.53  tms: 0.00  mit: 0.21  mip: 0.04
 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 

	 40.0 %: cytoplasmic
	 40.0 %: nuclear
	  8.0 %: cytoskeletal
	  4.0 %: extracellular, including cell wall
	  4.0 %: mitochondrial
	  4.0 %: vacuolar

>> prediction for Contig-U06239-1 is cyt
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