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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
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Contig-U06578-1
Contig ID Contig-U06578-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06578-1 (Contig-U06578-1Q) /CSM_Contig/Contig-U06578-1Q.Seq.d
AAAATAACATATATACTCATATTCAATTTCAAATTCAATTTCATTCATTG
TTGTCATTTATAGTAAAAATTACAAAAATAATTACAAATAAAATCTCAAA
AAAAAA
Gap no gap
Contig length 106
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 5390881
End point 5390775
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U06578
List of clone(s) 

est1=VSD639F,1,107
Translated Amino Acid sequence 
NNIYTHIQFQIQFHSLLSFIVKITKIITNKISKK
Translated Amino Acid sequence (All Frames) 
Frame A:
kityilifnfkfnfihcchl**klqk*lqiksqkk


Frame B:
k*hiysysisnsisfivviysknyknnyk*nlkkk


Frame C:
NNIYTHIQFQIQFHSLLSFIVKITKIITNKISKK
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06578-1 (Contig-U06578-1Q)
/CSM_Contig/Contig-U06578-1Q.Seq.d
         (106 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06578-1 (Contig-U06578-1Q) /CSM_Contig/Conti...   127  2e-30
Contig-U12541-1 (Contig-U12541-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U10850-1 (Contig-U10850-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U11864-1 (Contig-U11864-1Q) /CSM_Contig/Conti...    34  0.026
Contig-U02803-1 (Contig-U02803-1Q) /CSM_Contig/Conti...    34  0.026
Contig-U00222-1 (Contig-U00222-1Q) /CSM_Contig/Conti...    34  0.026
Contig-U12716-1 (Contig-U12716-1Q) /CSM_Contig/Conti...    32  0.10
Contig-U12264-1 (Contig-U12264-1Q) /CSM_Contig/Conti...    32  0.10
Contig-U09415-1 (Contig-U09415-1Q) /CSM_Contig/Conti...    32  0.10
Contig-U06330-1 (Contig-U06330-1Q) /CSM_Contig/Conti...    32  0.10

>Contig-U06578-1 (Contig-U06578-1Q) /CSM_Contig/Contig-U06578-1Q.Seq.d
          Length = 106

 Score =  127 bits (64), Expect = 2e-30
 Identities = 64/64 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  aaaataacatatatactcatattcaatttcaaattcaatttcattcattgttgtcattta 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  aaaataacatatatactcatattcaatttcaaattcaatttcattcattgttgtcattta 60

              
Query: 61 tagt 64
          ||||
Sbjct: 61 tagt 64


>Contig-U12541-1 (Contig-U12541-1Q) /CSM_Contig/Contig-U12541-1Q.Seq.d
          Length = 1390

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

                             
Query: 28  ttcaaattcaatttcatt 45
           ||||||||||||||||||
Sbjct: 880 ttcaaattcaatttcatt 897


>Contig-U10850-1 (Contig-U10850-1Q) /CSM_Contig/Contig-U10850-1Q.Seq.d
          Length = 1306

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

                             
Query: 23  tcaatttcaaattcaatt 40
           ||||||||||||||||||
Sbjct: 278 tcaatttcaaattcaatt 261


  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: 1792
Number of Sequences: 6905
Number of extensions: 1792
Number of successful extensions: 677
Number of sequences better than 10.0: 238
length of query: 106
length of database: 5,674,871
effective HSP length: 14
effective length of query: 92
effective length of database: 5,578,201
effective search space: 513194492
effective search space used: 513194492
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 2008.11. 9
Homology vs DNA 
Query= Contig-U06578-1 (Contig-U06578-1Q) /CSM_Contig/Contig-U06578-1Q.Seq.d
         (106 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

(AU264349) Dictyostelium discoideum vegetative cDNA clone:VS...   127   7e-26  1
(AC176328) Strongylocentrotus purpuratus clone R3-3054O20, W...    48   0.053  1
(AC176024) Strongylocentrotus purpuratus clone R3-3024L3, WO...    48   0.053  1
(EU070553) Eryngium coronatum rps16-trnK intergenic spacer, ...    46   0.21   1
(DQ832498) Eryngium coronatum rps16-trnK intergenic spacer, ...    46   0.21   1
(AY147573) Cypripedium passerinum cytochrome b-559 alpha sub...    46   0.21   1
(AC125478) Medicago truncatula clone mth2-31i19, complete se...    46   0.21   1
(AR553812) Sequence 8943 from patent US 6747137.                   46   0.21   1
(AC112619) Rattus norvegicus clone CH230-233I2, *** SEQUENCI...    46   0.21   1
(AC094884) Rattus norvegicus clone CH230-5O16, *** SEQUENCIN...    46   0.21   1
(AC225329) Solanum lycopersicum chromosome 9 clone C09SLe007...    46   0.21   1
(AC184303) Strongylocentrotus purpuratus clone R3-15H3, WORK...    46   0.21   1
(AC181680) Strongylocentrotus purpuratus clone R3-3090M22, W...    46   0.21   1
(AC180037) Strongylocentrotus purpuratus clone R3-3030O08, W...    46   0.21   1
(AC180017) Strongylocentrotus purpuratus clone R3-23H22, WOR...    46   0.21   1
(EK579666) 1095521409324 Global-Ocean-Sampling_GS-32-01-01-1...    46   0.21   1
(ED661176) GM_WBa0084D05.f GM_WBa Glycine max genomic clone ...    46   0.21   1
(AL423463) T3 end of clone AZ0AA008F04 of library AZ0AA from...    46   0.21   1
(CR323392) mte1-50K17RM1 BAC end, cultivar Jemalong A17 of M...    46   0.21   1
(EE637873) CHEL9282.b1_C17.ab1 CHE(LMS) serpentine sunflower...    46   0.21   1
(EE637497) CHEL8941.b1_J03.ab1 CHE(LMS) serpentine sunflower...    46   0.21   1
(EE632575) CHEL10492.b1_H07.ab1 CHE(LMS) serpentine sunflowe...    46   0.21   1
(AZ930743) 474.dhz58b03.s1 Saccharomyces unisporus NRRL Y-15...    38   0.62   2
(BX005016) Zebrafish DNA sequence from clone DKEY-104E13 in ...    44   0.83   1
(AC188388) Gallus gallus BAC clone CH261-117F4 from chromoso...    44   0.83   1
(AC187362) Gallus gallus BAC clone CH261-44J2 from chromosom...    44   0.83   1
(AC158563) Mus musculus chromosome 15, clone RP24-143I20, co...    44   0.83   1
(AC122832) Mus musculus BAC clone RP23-179D3 from 12, comple...    44   0.83   1
(AM480414) Vitis vinifera contig VV78X173878.33, whole genom...    44   0.83   1
(AC103512) Rattus norvegicus clone CH230-102H5, *** SEQUENCI...    44   0.83   1
(AC209324) Zea mays chromosome 5 clone CH201-114D5; ZMMBBc01...    44   0.83   1
(AC201521) Strongylocentrotus purpuratus clone R3-3089O18, W...    44   0.83   1
(AC201377) Strongylocentrotus purpuratus clone R3-17F1, WORK...    44   0.83   1
(AC179986) Strongylocentrotus purpuratus clone R3-3036H02, W...    44   0.83   1
(AC179744) Strongylocentrotus purpuratus clone R3-1018G23, W...    44   0.83   1
(AC178791) Strongylocentrotus purpuratus clone R3-29N6, WORK...    44   0.83   1
(AC178642) Strongylocentrotus purpuratus clone R3-11C23, WOR...    44   0.83   1
(FI039912) CHO_OF6463xh09f1.ab1 CHO_OF6 Nicotiana tabacum ge...    44   0.83   1
(FI033821) CHO_OF6446xb10r1.ab1 CHO_OF6 Nicotiana tabacum ge...    44   0.83   1
(FH679870) CHO_OF5059xc19f1.ab1 CHO_OF5 Nicotiana tabacum ge...    44   0.83   1
(FH430314) CHO_OF4925xh01r1.ab1 CHO_OF4 Nicotiana tabacum ge...    44   0.83   1
(AL978627) Danio rerio genomic clone DKEY-28H21, genomic sur...    44   0.83   1
(EI467144) PV_GBa0073G08.r PV_GBa Phaseolus vulgaris genomic...    44   0.83   1
(DE390751) Bombyx mori genomic DNA, BAC clone:12G1F.               44   0.83   1
(EL456687) CHTM9755.b1_F15.ab1 CHT(LMS) Jerusalem artichoke ...    44   0.83   1
(EH789895) CNSS29939.b1_F22.ab1 CNS(LMS) yellow starthistle ...    44   0.83   1
(EH789811) CNSS29854.b1_K24.ab1 CNS(LMS) yellow starthistle ...    44   0.83   1
(EH783911) CNSS23145.b1_B03.ab1 CNS(LMS) yellow starthistle ...    44   0.83   1
(EH773477) CNSM5912.b1_P13.ab1 CNS(LMS) yellow starthistle C...    44   0.83   1
(EH771635) CNSM4225.b1_A01.ab1 CNS(LMS) yellow starthistle C...    44   0.83   1
(EG676547) RCRDH16TP Castor bean cDNA library from roots, 1....    44   0.83   1
(CU554506) Spc_A1CH11 cDNA clone of Developmental Stages Lib...    44   0.83   1
(CF981389) yaa04c12.y1 RcSeed Ricinus communis cDNA 5', mRNA...    44   0.83   1
(EY436151) qm_NP32R.D02 Milwaukee estuary quagga mussel gill...    44   0.83   1
(AE000783) Borrelia burgdorferi B31, complete genome.              44   0.83   1
(AC169854) Macaca mulatta clone CH250-253A1, *** SEQUENCING ...    40   0.84   2
(AC201169) Strongylocentrotus purpuratus clone R3-14K15, WOR...    36   0.90   3
(EU643477) Adineta vaga clone Av_TEL_K_A retrotransposons Ju...    40   1.6    2
(AC147007) Medicago truncatula clone mth2-26c3, complete seq...    38   2.1    3
(AC201338) Strongylocentrotus purpuratus clone R3-16N6, WORK...    40   2.1    2
(BH533121) BOHHX03TR BOHH Brassica oleracea genomic clone BO...    34   2.2    2
(BH478006) BOGBG91TF BOGB Brassica oleracea genomic clone BO...    34   2.2    2
(BH742046) gt41a08.g1 BoBuds01 Brassica oleracea genomic clo...    34   2.2    2
(AC133028) Rattus norvegicus clone CH230-481F10, *** SEQUENC...    40   2.8    2
(AG242439) Lotus japonicus DNA, clone:LjT10l18_sfi.                32   2.9    2
(CR940311) M.truncatula DNA sequence from clone MTH2-17E17 o...    42   3.3    1
(Z74032) Caenorhabditis elegans Cosmid F35B12.                     42   3.3    1
(U29612) Caenorhabditis elegans cosmid C09B8, complete seque...    42   3.3    1
(CR932557) Paramecium tetraurelia, Small GTPase rab, putativ...    42   3.3    1
(AE014822) Plasmodium falciparum 3D7 chromosome 14 section 7...    42   3.3    1
(AC068130) Homo sapiens BAC clone RP11-640F22 from 2, comple...    42   3.3    1
(AC073969) Homo sapiens chromosome 2 clone RP11-164P17, WORK...    42   3.3    1
(CU326354) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   3.3    1
(AC191469) Muntiacus reevesi clone CH245-307M6, WORKING DRAF...    42   3.3    1
(AC185365) Muntiacus muntjak vaginalis clone CH244-114L17, W...    42   3.3    1
(AC184671) Strongylocentrotus purpuratus clone R3-1005K6, WO...    42   3.3    1
(AC184628) Strongylocentrotus purpuratus clone R3-1032B22, W...    42   3.3    1
(AC184600) Strongylocentrotus purpuratus clone R3-4018J4, WO...    42   3.3    1
(AC184497) Strongylocentrotus purpuratus clone R3-1109M8, WO...    42   3.3    1
(AC181836) Strongylocentrotus purpuratus clone R3-1022L20, W...    42   3.3    1
(AC180016) Strongylocentrotus purpuratus clone R3-3036O04, W...    42   3.3    1
(AC179823) Strongylocentrotus purpuratus clone R3-1012M2, WO...    42   3.3    1
(AC179606) Strongylocentrotus purpuratus clone R3-1028P05, W...    42   3.3    1
(AC178981) Strongylocentrotus purpuratus clone R3-3122G2, WO...    42   3.3    1
(AC178976) Strongylocentrotus purpuratus clone R3-3122C2, WO...    42   3.3    1
(AC178250) Strongylocentrotus purpuratus clone R3-3086L3, WO...    42   3.3    1
(AC177277) Strongylocentrotus purpuratus clone R3-44D7, WORK...    42   3.3    1
(AC177089) Strongylocentrotus purpuratus clone R3-4012A24, W...    42   3.3    1
(AC176685) Strongylocentrotus purpuratus clone R3-3088D24, W...    42   3.3    1
(AC176270) Strongylocentrotus purpuratus clone R3-3060A13, W...    42   3.3    1
(AC175896) Strongylocentrotus purpuratus clone R3-14O15, WOR...    42   3.3    1
(AC172421) Strongylocentrotus purpuratus clone R3-14J17, WOR...    42   3.3    1
(AC168421) Strongylocentrotus purpuratus clone R3-39O20, WOR...    42   3.3    1
(AM634788) Entamoeba dispar GSS, clone dispar128a05.p1k.           42   3.3    1
(AM633460) Entamoeba dispar GSS, clone dispar101e07.q1k.           42   3.3    1
(EI927043) VUH2-66H10TR VUUBBa (VUH2) Vigna unguiculata geno...    42   3.3    1
(EI881265) CAH1-65F19TR CAA1Ba Cicer arietinum genomic clone...    42   3.3    1
(EI602591) Wang-VSVGgfp-Jurkat-454-Mse-023556_2164_2185 Wang...    42   3.3    1
(ED813694) ML__Ba0085C22f ML__Ba Mimulus lewisii genomic, ge...    42   3.3    1
(ED813215) ML__Ba0080A06r ML__Ba Mimulus lewisii genomic, ge...    42   3.3    1

>(AU264349) Dictyostelium discoideum vegetative cDNA clone:VSD639,
          5' end single read.
          Length = 107

 Score =  127 bits (64), Expect = 7e-26
 Identities = 64/64 (100%)
 Strand = Plus / Plus


Query: 1  aaaataacatatatactcatattcaatttcaaattcaatttcattcattgttgtcattta 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  aaaataacatatatactcatattcaatttcaaattcaatttcattcattgttgtcattta 60


Query: 61 tagt 64
          ||||
Sbjct: 61 tagt 64

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 93,813,251
Number of extensions: 6531745
Number of successful extensions: 1989482
Number of sequences better than 10.0: 135
Length of query: 106
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 84
Effective length of database: 93,199,600,587
Effective search space: 7828766449308
Effective search space used: 7828766449308
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06578-1 (Contig-U06578-1Q) /CSM_Contig/Contig-U06578-1Q.Seq.d
         (106 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 61,695,285
Number of extensions: 286016
Number of successful extensions: 510
Number of sequences better than 10.0: 0
Number of HSP's gapped: 510
Number of HSP's successfully gapped: 0
Length of query: 35
Length of database: 1,040,966,779
Length adjustment: 9
Effective length of query: 26
Effective length of database: 1,012,128,214
Effective search space: 26315333564
Effective search space used: 26315333564
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: 0.90  gvh: 0.45  alm: 0.39  top: 0.60  tms: 0.00  mit: 0.43  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.40  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 

	 48.0 %: mitochondrial
	 20.0 %: cytoplasmic
	 16.0 %: nuclear
	  8.0 %: vacuolar
	  4.0 %: cytoskeletal
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U06578-1 is mit
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