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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-U02225-1
Contig ID Contig-U02225-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U02225-1 (Contig-U02225-1Q) /CSM_Contig/Contig-U02225-1Q.Seq.d
ATTTCAATAAACACCTTTATATTTACCCCCTTTTCTATTTATCTATTTAT
TTACTTTTTTTTTTGGNTTTTTTTATCATCATCACCATCATNGTTTTTTT
TATTNATAATTTNGNAATTTTTNAAATTTTAAATTTTTTTTTTTTTTTNG
GGGGGGGAAAAAACCCTTTTTTTNAAATTTTTTTCCATNCNTTTTTTTTT
NC----------TATTTGTAATTTTGTAATTTTTTAAATTTTAAATTTTT
TTTTTTTTTTTCGTGTGTGATATAAACCTTTTTTTTTAATTTTTTTTCAT
TCATTTTTTTTTTACATATAAATATAAATAAATAATAATAATAATACACA
TTACACATTTATTTTAATAAAAGAAAAATAATAAATAAATAAATAAATAA
ATAAAAAATTTTTTTAAAAAAAAATTAAATAAAAATTAAATTTGTAATAT
TAAAAAAAAAAAAAAAAAAATCGAAAAATAATAAGGAAGTAATACCATTT
TATTTGAAAAAAAAAAAAAAAAAAAATCAAATCAAATCAAATCAAATCTT
CCATTACTATTATTGGTATCATTACTCTAGTGGGTTTAAATAATTAAATA
AATAATCAATCTACCAAACAAACAAATAAACAAATAAAATC
Gap gap included
Contig length 631
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 3180900
End point 3181440
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 3
Link to clone list U02225
List of clone(s) 

est1=VSG137F,1,203
est2=VSC705Z,204,633
est3=VSG137Z,216,416
Translated Amino Acid sequence 
FNKHLYIYPLFYLSIYLLFFLXFFIIITIXVFFIXNXXIFXILNFFFFXGGGKNPFFXIF
FHXFFF---

---ICNFVIF*ilnfffffrv*ykpffliffhsfffyi*i*innnnnthytfilikek**
ink*inkkff*kkik*klnl*y*kkkkknrkiirk*yhfi*kkkkkkiksnqikssitii
giitlvglnn*innqstkqtnkqik
Translated Amino Acid sequence (All Frames) 
Frame A:
isintfiftpfsiylfiyfffwxflssspsxfflxiixxfxkf*iffffxggektlfxkf
fsxxffx---

---yl*fcnflnfkfffffscvi*tfffnffsfifflhinink****ytlhiyfnkrkii
nk*ink*kiflkkn*ikikfvilkkkkkksknnkevipfylkkkkkknqiksnqifhyyy
wyhyssgfk*lnk*siyqtnk*tnki

Frame B:
fq*tplylppflfiylftfffgffyhhhhhxffyx*fxnfxnfkfffffxggkkpffxnf
fpxxffx---

---ICNFVIF*ilnfffffrv*ykpffliffhsfffyi*i*innnnnthytfilikek**
ink*inkkff*kkik*klnl*y*kkkkknrkiirk*yhfi*kkkkkkiksnqikssitii
giitlvglnn*innqstkqtnkqik

Frame C:
FNKHLYIYPLFYLSIYLLFFLXFFIIITIXVFFIXNXXIFXILNFFFFXGGGKNPFFXIF
FHXFFF---

---fvil*ffkf*ifffffvcdinlff*fffihffftykyk*iiiiihithlf**kknnk
*ink*iknffkkklnkn*icnikkkkkkiek**gsntilfekkkkkksnqiksnlpllll
vsll*wv*iik*iinlpnkqink*n
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U02225-1 (Contig-U02225-1Q)
/CSM_Contig/Contig-U02225-1Q.Seq.d
         (641 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U02225-1 (Contig-U02225-1Q) /CSM_Contig/Conti...   125  6e-29
Contig-U14162-1 (Contig-U14162-1Q) /CSM_Contig/Conti...    44  2e-04
Contig-U11158-1 (Contig-U11158-1Q) /CSM_Contig/Conti...    44  2e-04
Contig-U09772-1 (Contig-U09772-1Q) /CSM_Contig/Conti...    42  7e-04
Contig-U14242-1 (Contig-U14242-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U09114-1 (Contig-U09114-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U14463-1 (Contig-U14463-1Q) /CSM_Contig/Conti...    36  0.045
Contig-U13153-1 (Contig-U13153-1Q) /CSM_Contig/Conti...    36  0.045
Contig-U12474-1 (Contig-U12474-1Q) /CSM_Contig/Conti...    36  0.045
Contig-U12019-1 (Contig-U12019-1Q) /CSM_Contig/Conti...    36  0.045

>Contig-U02225-1 (Contig-U02225-1Q) /CSM_Contig/Contig-U02225-1Q.Seq.d
          Length = 641

 Score =  125 bits (63), Expect = 6e-29
 Identities = 63/63 (100%)
 Strand = Plus / Plus

                                                                       
Query: 527 tcaaatcaaatcaaatcaaatcttccattactattattggtatcattactctagtgggtt 586
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 527 tcaaatcaaatcaaatcaaatcttccattactattattggtatcattactctagtgggtt 586

              
Query: 587 taa 589
           |||
Sbjct: 587 taa 589


 Score =  107 bits (54), Expect = 1e-23
 Identities = 54/54 (100%)
 Strand = Plus / Plus

                                                                
Query: 1  atttcaataaacacctttatatttacccccttttctatttatctatttatttac 54
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atttcaataaacacctttatatttacccccttttctatttatctatttatttac 54


 Score = 71.9 bits (36), Expect = 8e-13
 Identities = 36/36 (100%)
 Strand = Plus / Plus

                                               
Query: 471 tcgaaaaataataaggaagtaataccattttatttg 506
           ||||||||||||||||||||||||||||||||||||
Sbjct: 471 tcgaaaaataataaggaagtaataccattttatttg 506


 Score = 40.1 bits (20), Expect = 0.003
 Identities = 51/59 (86%)
 Strand = Plus / Plus

                                                                      
Query: 75  atcatcatcaccatcatngnnnnnnnnattnataatttngnaatttttnaaattttaaa 133
           |||||||||||||||||||        ||||||||||||||||||||||||||||||||
Sbjct: 75  atcatcatcaccatcatngttttttttattnataatttngnaatttttnaaattttaaa 133


 Score = 38.2 bits (19), Expect = 0.011
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 213 tatttgtaattttgtaatt 231
           |||||||||||||||||||
Sbjct: 213 tatttgtaattttgtaatt 231


 Score = 36.2 bits (18), Expect = 0.045
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 347 cacattacacatttattt 364
           ||||||||||||||||||
Sbjct: 347 cacattacacatttattt 364


 Score = 34.2 bits (17), Expect = 0.18
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 150 ggggggggaaaaaaccc 166
           |||||||||||||||||
Sbjct: 150 ggggggggaaaaaaccc 166


>Contig-U14162-1 (Contig-U14162-1Q) /CSM_Contig/Contig-U14162-1Q.Seq.d
          Length = 1182

 Score = 44.1 bits (22), Expect = 2e-04
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                  
Query: 527  tcaaatcaaatcaaatcaaatc 548
            ||||||||||||||||||||||
Sbjct: 1037 tcaaatcaaatcaaatcaaatc 1058


 Score = 44.1 bits (22), Expect = 2e-04
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                  
Query: 527  tcaaatcaaatcaaatcaaatc 548
            ||||||||||||||||||||||
Sbjct: 1032 tcaaatcaaatcaaatcaaatc 1053


 Score = 44.1 bits (22), Expect = 2e-04
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                  
Query: 527  tcaaatcaaatcaaatcaaatc 548
            ||||||||||||||||||||||
Sbjct: 1042 tcaaatcaaatcaaatcaaatc 1063


 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                
Query: 527  tcaaatcaaatcaaatcaaa 546
            ||||||||||||||||||||
Sbjct: 1047 tcaaatcaaatcaaatcaaa 1066


 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                
Query: 529  aaatcaaatcaaatcaaatc 548
            ||||||||||||||||||||
Sbjct: 1029 aaatcaaatcaaatcaaatc 1048


>Contig-U11158-1 (Contig-U11158-1Q) /CSM_Contig/Contig-U11158-1Q.Seq.d
          Length = 3221

 Score = 44.1 bits (22), Expect = 2e-04
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                  
Query: 527  tcaaatcaaatcaaatcaaatc 548
            ||||||||||||||||||||||
Sbjct: 3143 tcaaatcaaatcaaatcaaatc 3164


 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                
Query: 529  aaatcaaatcaaatcaaatc 548
            ||||||||||||||||||||
Sbjct: 3140 aaatcaaatcaaatcaaatc 3159


 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                
Query: 527  tcaaatcaaatcaaatcaaa 546
            ||||||||||||||||||||
Sbjct: 3148 tcaaatcaaatcaaatcaaa 3167


  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: 5442
Number of Sequences: 6905
Number of extensions: 5442
Number of successful extensions: 745
Number of sequences better than 10.0: 142
length of query: 641
length of database: 5,674,871
effective HSP length: 16
effective length of query: 625
effective length of database: 5,564,391
effective search space: 3477744375
effective search space used: 3477744375
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2009. 5.16
Homology vs DNA 
Query= Contig-U02225-1 (Contig-U02225-1Q) /CSM_Contig/Contig-U02225-1Q.Seq.d
         (641 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

(AU266021) Dictyostelium discoideum vegetative cDNA clone:VS...   107   5e-19  1
(AU262737) Dictyostelium discoideum vegetative cDNA clone:VS...    76   2e-09  1
(AE014850) Plasmodium falciparum 3D7 chromosome 12, section ...    44   0.24   2
(AC090654) Mus musculus strain C57BL/6J clone rp23-329p1 map...    48   0.42   1
(AC092252) Mus musculus clone RP23-355P17, WORKING DRAFT SEQ...    48   0.42   1
(AC223244) Bos taurus clone CH240-425I10, WORKING DRAFT SEQU...    48   0.42   1
(BX005079) Zebrafish DNA sequence from clone CH211-176D9.          46   1.6    1
(AC201284) Strongylocentrotus purpuratus clone R3-16E7, WORK...    46   1.6    1
(AC192504) Cavia porcellus clone CH234-373M21, WORKING DRAFT...    46   1.6    1
(AC192486) Cavia porcellus clone CH234-124K20, WORKING DRAFT...    46   1.6    1
(ER877090) MUGQ_CH252P266L08T7_CN551_022 CHORI-252 Vervet Mo...    46   1.6    1
(DX563383) MUGQ_CH252P037I22T7_AV831_087 CHORI-252 Vervet Mo...    46   1.6    1
(DX525276) GH_MBb0062O18r GH_MBb Gossypium hirsutum genomic ...    46   1.6    1
(FK758941) av02067l14r1.1 Symbiotic sea anemone (Anemonia vi...    46   1.6    1
(FK749130) av01004a16r1.1 Symbiotic sea anemone (Anemonia vi...    46   1.6    1
(FK748859) av01043j05r1.1 Symbiotic sea anemone (Anemonia vi...    46   1.6    1
(FK729302) av02077a20r1.1 Symbiotic sea anemone (Anemonia vi...    46   1.6    1
(FK722182) av01028l19r1.1 Symbiotic sea anemone (Anemonia vi...    46   1.6    1
(AC068995) Homo sapiens chromosome 3 clone RP11-463G10, WORK...    40   2.6    2
(DU518876) 1098609829804 CHORI-243 Ovis aries genomic clone ...    38   3.2    2
(DU438468) 1098421027416 CHORI-243 Ovis aries genomic clone ...    38   3.4    2
(DE500858) Bombyx mori genomic DNA, Fosmid clone:GBMFno112_g...    32   4.3    2
(AC022443) Homo sapiens chromosome 5 clone RP11-36C20, compl...    42   6.4    2
(CR392011) Zebrafish DNA sequence from clone DKEY-272L17 in ...    44   6.5    1
(BX571977) Zebrafish DNA sequence from clone DKEY-9E15 in li...    44   6.5    1
(BX294131) Zebrafish DNA sequence from clone CH211-254O18 in...    44   6.5    1
(AC140947) Gallus gallus BAC clone TAM33-40B24 from chromoso...    44   6.5    1
(AC158786) Mus musculus chromosome 5, clone RP23-228M24, com...    44   6.5    1
(AC132347) Mus musculus BAC clone RP24-186F6 from chromosome...    44   6.5    1
(AC098716) Mus musculus BAC clone RP23-2F19 from 9, complete...    44   6.5    1
(AC093341) Mus musculus chromosome 5, clone RP23-7E4, comple...    44   6.5    1
(AM472809) Vitis vinifera contig VV78X138658.6, whole genome...    44   6.5    1
(CS104292) Sequence 12 from Patent WO2005047318.                   44   6.5    1
(CQ870010) Sequence 431 from Patent WO2004074320.                  44   6.5    1
(AP001120) Homo sapiens genomic DNA, chromosome 18 clone:RP1...    44   6.5    1
(AC010321) Homo sapiens chromosome 16 clone CTD-2540M10, com...    44   6.5    1
(AC138870) Homo sapiens chromosome 16 clone RP11-144I23, WOR...    44   6.5    1
(AC133059) Rattus norvegicus clone CH230-14O22, *** SEQUENCI...    44   6.5    1
(AC132792) Rattus norvegicus clone CH230-234G1, *** SEQUENCI...    44   6.5    1
(AC128932) Rattus norvegicus clone CH230-369C15, WORKING DRA...    44   6.5    1
(AC115206) Rattus norvegicus clone CH230-375C19, *** SEQUENC...    44   6.5    1
(AC111227) Rattus norvegicus clone CH230-110E17, WORKING DRA...    44   6.5    1
(AC100972) Mus musculus clone RP23-75K6, LOW-PASS SEQUENCE S...    44   6.5    1
(AC098250) Rattus norvegicus clone CH230-1H17, *** SEQUENCIN...    44   6.5    1
(AC097270) Pan troglodytes clone RP43-35J14, WORKING DRAFT S...    44   6.5    1
(CU856477) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   6.5    1
(CU469491) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   6.5    1
(AC221419) Bos taurus clone CH240-406K4, WORKING DRAFT SEQUE...    44   6.5    1
(AC197749) Macaca mulatta chromosome UNK clone CH250-151F7, ...    44   6.5    1
(AC172182) Atelerix albiventris clone LB4-447B10, WORKING DR...    44   6.5    1
(AC009454) Homo sapiens chromosome 18 clone RP11-78A19 map 1...    44   6.5    1
(AC005140) Plasmodium falciparum chromosome 12 clone PFYACB8...    44   6.5    1
(AC005139) Plasmodium falciparum chromosome 12, *** SEQUENCI...    44   6.5    1
(FI311213) AdH1186-CPY2-F11TR AdH1 Arachis duranensis genomi...    44   6.5    1
(FI282187) AdH1028-CPY2-J12TF AdH1 Arachis duranensis genomi...    44   6.5    1
(FI280089) AdH1001-CPY2-L5TR AdH1 Arachis duranensis genomic...    44   6.5    1
(ET436666) MUGQ_CH252P438F13T7_CP841_059 CHORI-252 Vervet Mo...    44   6.5    1
(ED658075) GM_WBa0078K09.r GM_WBa Glycine max genomic clone ...    44   6.5    1
(DE194803) Branchiostoma floridae DNA, clone: CH302-076_L24_...    44   6.5    1
(DE192522) Branchiostoma floridae DNA, clone: CH302-072_P21_...    44   6.5    1
(CT083422) Sus scrofa genomic clone PigE-264A2, genomic surv...    44   6.5    1
(CT083413) Sus scrofa genomic clone PigE-264A1, genomic surv...    44   6.5    1
(CL642345) CH213-28C08.SP6 CH213 Gasterosteus aculeatus geno...    44   6.5    1
(CL374877) RPCI44_470L4.f RPCI-44 Sus scrofa genomic clone R...    44   6.5    1
(CE407641) tigr-gss-dog-17000335715987 Dog Library Canis lup...    44   6.5    1
(CE025444) tigr-gss-dog-17000322368408 Dog Library Canis lup...    44   6.5    1
(DN040074) JGI_CABA398.fwd NIH_XGC_tropKid1 Xenopus (Siluran...    44   6.5    1
(DN040073) JGI_CABA398.rev NIH_XGC_tropKid1 Xenopus (Siluran...    44   6.5    1
(CR574427) Xenopus tropicalis EST, clone THdA023j21 3'.            44   6.5    1
(CK953713) 4093451 BARC 10BOV Bos taurus cDNA clone 10BOV31_...    44   6.5    1
(BY094208) Mus musculus 17 days embryo whole body cDNA, RIKE...    44   6.5    1
(FG086804) CMRC-FF-IH0-acf-a-04-0-CMRC.r1 Ceratitis capitata...    44   6.5    1
(FE743067) CAYC1307.b1 CAYC Petrolisthes cinctipes heart, ne...    44   6.5    1
(AC114299) Homo sapiens chromosome 5 clone RP11-12L7, WORKIN...    42   7.8    2

>(AU266021) Dictyostelium discoideum vegetative cDNA clone:VSG137,
          5' end single read.
          Length = 203

 Score =  107 bits (54), Expect = 5e-19
 Identities = 54/54 (100%)
 Strand = Plus / Plus


Query: 1  atttcaataaacacctttatatttacccccttttctatttatctatttatttac 54
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atttcaataaacacctttatatttacccccttttctatttatctatttatttac 54

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 116,375,004
Number of extensions: 7015475
Number of successful extensions: 654892
Number of sequences better than 10.0: 77
Length of query: 641
Length of database: 101,790,757,118
Length adjustment: 24
Effective length of query: 617
Effective length of database: 99,340,224,878
Effective search space: 61292918749726
Effective search space used: 61292918749726
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.19
Homology vs Protein 
Query= Contig-U02225-1 (Contig-U02225-1Q) /CSM_Contig/Contig-U02225-1Q.Seq.d
         (641 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: 245,406,132
Number of extensions: 2220606
Number of successful extensions: 2985
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2954
Number of HSP's successfully gapped: 0
Length of query: 213
Length of database: 1,051,180,864
Length adjustment: 123
Effective length of query: 90
Effective length of database: 653,084,107
Effective search space: 58777569630
Effective search space used: 58777569630
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: 31 (16.5 bits)
PSORT 

 psg: 1.00  gvh: 0.57  alm: 0.15  top: 0.47  tms: 0.13  mit: 0.34  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: 1.00  m3b: 0.00  m_ : 0.00 

	 32.0 %: endoplasmic reticulum
	 28.0 %: mitochondrial
	 16.0 %: plasma membrane
	  8.0 %: extracellular, including cell wall
	  4.0 %: Golgi
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system
	  4.0 %: cytoplasmic

>> prediction for Contig-U02225-1 is end
VS (DIR, S) 2
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