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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U06785-1
Contig ID Contig-U06785-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06785-1 (Contig-U06785-1Q) /CSM_Contig/Contig-U06785-1Q.Seq.d
TTAATTGAAAATGTATTAATTACTTCATTGGTAACTTTAGCATATATGTC
ATTTAGAGTTAGAAGAAATAAATTAACCAATTGGATGCCAGTATTTCGTG
GTAATAGAAAGCTTAATGTAAATAGCACCTTAATAATCACAGTATTACTT
ACAATTTTAAATGATAAAACCAATAAACAAATCTTTAATCTCGATGCCAA
AGAACTCTATATTAAATATTTTTCAATATTTGAACCAAAAGATTTTGATA
AACATTTTAATGCTTGGTACAGATTTTCAATTTCCGTGGTTCCATTATTA
TTTATTCCATCAAGATTGTATTTTATTATTCCTTATTTTATTTCAACTAC
TATCATACCTTTAAAAAATCAATTGATAGATAATTCATATTATAAATAAA
AAAATAAAAATAATAAACTATTATTTAATAAAATAAAAAATNNAANAATA
AAAAAAAA
Gap no gap
Contig length 458
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 3170065
End point 3169607
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U06785
List of clone(s) 

est1=VSG231F,-1,459
est2=VSG231Z,194,396
Translated Amino Acid sequence 
LIENVLITSLVTLAYMSFRVRRNKLTNWMPVFRGNRKLNVNSTLIITVLLTILNDKTNKQ
IFNLDAKELYIKYFSIFEPKDFDKHFNAWYRFSISVVPLLFIPSRLYFIIPYFISTTIIP
LKNQLIDNSYYK*knknnkllfnkiknxxikk
Translated Amino Acid sequence (All Frames) 
Frame A:
LIENVLITSLVTLAYMSFRVRRNKLTNWMPVFRGNRKLNVNSTLIITVLLTILNDKTNKQ
IFNLDAKELYIKYFSIFEPKDFDKHFNAWYRFSISVVPLLFIPSRLYFIIPYFISTTIIP
LKNQLIDNSYYK*knknnkllfnkiknxxikk


Frame B:
*lkmy*llhw*l*hichleleein*pigcqyfvvieslm*iap**sqyylqf*mikpink
slismpknsilnifqylnqkilinilmlgtdfqfpwfhyylfhqdcillflilfqllsyl
*kin**iihiinkkikiinyylik*kxxx*kk


Frame C:
n*kcinyfignfsiyvi*s*kk*inqldasisw**ka*ck*hlnnhsitynfk**nq*tn
l*srcqrtly*iffni*tkrf**tf*clvqifnfrgsiiiysikivfyyslfyfnyyhtf
kksidr*fil*ikk*k**tii**nkkxxnkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06785-1 (Contig-U06785-1Q)
/CSM_Contig/Contig-U06785-1Q.Seq.d
         (458 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06785-1 (Contig-U06785-1Q) /CSM_Contig/Conti...   573  e-164
Contig-U11030-1 (Contig-U11030-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U14513-1 (Contig-U14513-1Q) /CSM_Contig/Conti...    38  0.008
Contig-U14169-1 (Contig-U14169-1Q) /CSM_Contig/Conti...    36  0.032
Contig-U10654-1 (Contig-U10654-1Q) /CSM_Contig/Conti...    36  0.032
Contig-U00011-1 (Contig-U00011-1Q) /CSM_Contig/Conti...    36  0.032
Contig-U12633-1 (Contig-U12633-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U09104-1 (Contig-U09104-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U06379-1 (Contig-U06379-1Q) /CSM_Contig/Conti...    34  0.13

>Contig-U06785-1 (Contig-U06785-1Q) /CSM_Contig/Contig-U06785-1Q.Seq.d
          Length = 458

 Score =  573 bits (289), Expect = e-164
 Identities = 289/289 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ttaattgaaaatgtattaattacttcattggtaactttagcatatatgtcatttagagtt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ttaattgaaaatgtattaattacttcattggtaactttagcatatatgtcatttagagtt 60

                                                                       
Query: 61  agaagaaataaattaaccaattggatgccagtatttcgtggtaatagaaagcttaatgta 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  agaagaaataaattaaccaattggatgccagtatttcgtggtaatagaaagcttaatgta 120

                                                                       
Query: 121 aatagcaccttaataatcacagtattacttacaattttaaatgataaaaccaataaacaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 aatagcaccttaataatcacagtattacttacaattttaaatgataaaaccaataaacaa 180

                                                                       
Query: 181 atctttaatctcgatgccaaagaactctatattaaatatttttcaatatttgaaccaaaa 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 atctttaatctcgatgccaaagaactctatattaaatatttttcaatatttgaaccaaaa 240

                                                            
Query: 241 gattttgataaacattttaatgcttggtacagattttcaatttccgtgg 289
           |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 gattttgataaacattttaatgcttggtacagattttcaatttccgtgg 289


 Score = 32.2 bits (16), Expect = 0.49
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 345 aactactatcatacct 360
           ||||||||||||||||
Sbjct: 345 aactactatcatacct 360


>Contig-U11030-1 (Contig-U11030-1Q) /CSM_Contig/Contig-U11030-1Q.Seq.d
          Length = 1217

 Score = 40.1 bits (20), Expect = 0.002
 Identities = 23/24 (95%)
 Strand = Plus / Plus

                                   
Query: 225 aatatttgaaccaaaagattttga 248
           |||| |||||||||||||||||||
Sbjct: 131 aataattgaaccaaaagattttga 154


>Contig-U14513-1 (Contig-U14513-1Q) /CSM_Contig/Contig-U14513-1Q.Seq.d
          Length = 1225

 Score = 38.2 bits (19), Expect = 0.008
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                              
Query: 230 ttgaaccaaaagattttga 248
           |||||||||||||||||||
Sbjct: 767 ttgaaccaaaagattttga 749


  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: 6176
Number of Sequences: 6905
Number of extensions: 6176
Number of successful extensions: 666
Number of sequences better than 10.0: 224
length of query: 458
length of database: 5,674,871
effective HSP length: 16
effective length of query: 442
effective length of database: 5,564,391
effective search space: 2459460822
effective search space used: 2459460822
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-U06785-1 (Contig-U06785-1Q) /CSM_Contig/Contig-U06785-1Q.Seq.d
         (458 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

(AU266164) Dictyostelium discoideum vegetative cDNA clone:VS...   581   e-165  2
(BJ347217) Dictyostelium discoideum cDNA clone:dda26o07, 3' ...   581   e-164  2
(AU266165) Dictyostelium discoideum vegetative cDNA clone:VS...   133   3e-29  2
(BH126755) BARC-Satt589 Size-selected soybean genomic Glycin...    42   0.10   2
(AC216766) Populus trichocarpa clone POP029-O12, complete se...    38   0.16   2
(AC223734) Bos taurus clone CH240-459A22, WORKING DRAFT SEQU...    48   0.27   1
(DU936995) 368485 Tomato EcoRI BAC Library Solanum lycopersi...    40   0.53   2
(BZ467198) BONOB78TR BO_1.6_2_KB_tot Brassica oleracea genom...    46   1.1    1
(BQ434368) AGENCOURT_7831346 NIH_MGC_67 Homo sapiens cDNA cl...    46   1.1    1
(BQ451103) PfESToab03g12.y1 Plasmodium falciparum 3D7 asexua...    32   2.3    3
(AC098535) Rattus norvegicus clone CH230-89C2, *** SEQUENCIN...    38   2.4    4
(AC119503) Rattus norvegicus clone CH230-243I22, WORKING DRA...    36   2.7    3
(AP009356) Onion yellows phytoplasma OY-W genomic DNA, parti...    38   3.4    4
(AC184585) Strongylocentrotus purpuratus clone R3-3051D15, W...    42   4.2    4
(AL732493) Mouse DNA sequence from clone RP23-358F6 on chrom...    44   4.3    1
(AC103125) Rattus norvegicus clone CH230-213J15, *** SEQUENC...    44   4.3    1
(AC173605) Bos taurus clone CH240-300A9, WORKING DRAFT SEQUE...    44   4.3    1
(AZ385945) 1M0144K07R Mouse 10kb plasmid UUGC1M library Mus ...    44   4.3    1
(FH841742) OSB_1259003xg07r1.ab1 OSB_1259 Nicotiana tabacum ...    44   4.3    1
(ER623383) 1093017484710 Global-Ocean-Sampling_GS-36-01-01-2...    44   4.3    1
(ER446291) 1092963830394 Global-Ocean-Sampling_GS-35-01-01-1...    44   4.3    1
(EK406077) 1095505002907 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.3    1
(EK358071) 1095468739433 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.3    1
(AM651619) Entamoeba moshkovskii FIC GSS, clone mosh099b01.p1k.    44   4.3    1
(EJ673472) 1092955067362 Global-Ocean-Sampling_GS-30-02-01-1...    44   4.3    1
(EJ638126) 1093006415344 Global-Ocean-Sampling_GS-29-01-01-1...    44   4.3    1
(EJ337225) 1092963487751 Global-Ocean-Sampling_GS-28-01-01-1...    44   4.3    1
(EJ048459) 1095454131644 Global-Ocean-Sampling_GS-26-01-01-1...    44   4.3    1
(ED460045) AUAC-aac57e07.b1 Ascaris suum whole genome shotgu...    44   4.3    1
(AG575812) Mus musculus molossinus DNA, clone:MSMg01-499N03....    44   4.3    1
(CE804939) tigr-gss-dog-17000331467976 Dog Library Canis lup...    44   4.3    1
(CC454034) BARC-Satt681 Size-selected soybean genomic Glycin...    44   4.3    1
(BZ112349) CH230-210F11.TVB CHORI-230 Segment 1 Rattus norve...    44   4.3    1
(BZ101370) CH230-146J15.TJB CHORI-230 Segment 1 Rattus norve...    44   4.3    1
(CN447930) GUO_cDNA_24_82 Flower bud cDNA library from Lycor...    44   4.3    1
(FG978554) HTAO-aaa93h11.b1 Heterorhabditis_bacteriophora_ES...    44   4.3    1
(FG608127) stem_S031_E03.SEQ Opium poppy stem cDNA library P...    44   4.3    1
(FF680885) HTAO-aaa46b12.g1 Heterorhabditis_bacteriophora_ES...    44   4.3    1
(AC175814) Loxodonta africana clone VMRC15-600G15, WORKING D...    38   4.4    6
(AC212275) Solanum lycopersicum chromosome 5 clone C05MBoI00...    40   5.1    4
(AC159804) Glycine max clone gmp1-34b24, complete sequence.        36   5.4    5
(BB504875) Mus musculus 0 day neonate kidney cDNA, RIKEN ful...    34   5.5    2
(AG487468) Mus musculus molossinus DNA, clone:MSMg01-383O12....    34   5.7    2
(CU856653) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    34   6.4    3
(AC024699) Homo sapiens chromosome 8 clone RP11-37E7, WORKIN...    42   6.5    3
(AC158716) Rhinolophus ferrumequinum clone VMRC7-149J13, WOR...    38   6.6    4
(AC012232) Homo sapiens clone RP11-113C18, WORKING DRAFT SEQ...    38   6.8    4
(AC006764) Caenorhabditis elegans clone Y43B11, *** SEQUENCI...    32   7.7    2
(AC109186) Mus musculus chromosome 5, clone RP24-351E22, com...    40   7.9    3
(AC174581) Bos taurus clone CH240-293J4, WORKING DRAFT SEQUE...    42   8.0    3
(AC215897) Populus trichocarpa clone POP034-F24, complete se...    38   8.2    5
(AC162134) Loxodonta africana clone VMRC15-364M22, WORKING D...    38   8.4    6
(AC024780) Caenorhabditis elegans cosmid Y43B11AR, complete ...    32   9.0    2
(AC151152) Bos taurus clone CH240-386E17, WORKING DRAFT SEQU...    40   9.4    3

>(AU266164) Dictyostelium discoideum vegetative cDNA clone:VSG231,
           5' end single read.
          Length = 461

 Score =  581 bits (293), Expect(2) = e-165
 Identities = 293/293 (100%)
 Strand = Plus / Plus


Query: 1   ttaattgaaaatgtattaattacttcattggtaactttagcatatatgtcatttagagtt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 3   ttaattgaaaatgtattaattacttcattggtaactttagcatatatgtcatttagagtt 62


Query: 61  agaagaaataaattaaccaattggatgccagtatttcgtggtaatagaaagcttaatgta 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 63  agaagaaataaattaaccaattggatgccagtatttcgtggtaatagaaagcttaatgta 122


Query: 121 aatagcaccttaataatcacagtattacttacaattttaaatgataaaaccaataaacaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 123 aatagcaccttaataatcacagtattacttacaattttaaatgataaaaccaataaacaa 182


Query: 181 atctttaatctcgatgccaaagaactctatattaaatatttttcaatatttgaaccaaaa 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 183 atctttaatctcgatgccaaagaactctatattaaatatttttcaatatttgaaccaaaa 242


Query: 241 gattttgataaacattttaatgcttggtacagattttcaatttccgtggttcc 293
           |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 243 gattttgataaacattttaatgcttggtacagattttcaatttccgtggttcc 295

 Score = 36.2 bits (18), Expect(2) = e-165
 Identities = 18/18 (100%)
 Strand = Plus / Plus


Query: 344 caactactatcatacctt 361
           ||||||||||||||||||
Sbjct: 346 caactactatcatacctt 363

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 415,622,666
Number of extensions: 27837466
Number of successful extensions: 2395280
Number of sequences better than 10.0: 55
Length of query: 458
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 435
Effective length of database: 93,106,754,628
Effective search space: 40501438263180
Effective search space used: 40501438263180
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06785-1 (Contig-U06785-1Q) /CSM_Contig/Contig-U06785-1Q.Seq.d
         (458 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC079935_18(AC079935|pid:none) Genomic sequence for Oryza sativa...    35   1.1
CP000867_255(CP000867|pid:none) Methanococcus maripaludis C6, co...    34   1.8
BX950229_630(BX950229|pid:none) Methanococcus maripaludis strain...    33   2.4
AE017243_62(AE017243|pid:none) Mycoplasma hyopneumoniae J, compl...    32   5.2
AE016825_3988(AE016825|pid:none) Chromobacterium violaceum ATCC ...    32   6.8
CP000745_298(CP000745|pid:none) Methanococcus maripaludis C7, co...    32   6.8
BX950229_1047(BX950229|pid:none) Methanococcus maripaludis strai...    32   6.8
CP000745_1638(CP000745|pid:none) Methanococcus maripaludis C7, c...    32   6.8
AE017244_67(AE017244|pid:none) Mycoplasma hyopneumoniae 7448, co...    32   8.9
CR954246_2105(CR954246|pid:none) Pseudoalteromonas haloplanktis ...    32   8.9

>AC079935_18(AC079935|pid:none) Genomic sequence for Oryza sativa
           (japonica cultivar-group) cultivar Nipponbare clone
           OSJNBa0095C06, from Chromosome 10, complete sequence.
          Length = 586

 Score = 34.7 bits (78), Expect = 1.1
 Identities = 31/118 (26%), Positives = 58/118 (49%), Gaps = 13/118 (11%)
 Frame = -1

Query: 332 GIIKYNL-DGINN--NGTTEIENLYQALKCL--SKSFGSNIEKYLI*SSLASRLKICLLV 168
           GIIK+ L D IN+  NG  E+E L   +  L         I+K+           ICLL
Sbjct: 52  GIIKFELLDLINDFHNGFLEVERLNYGIVTLVPKTKDAEQIQKFR---------PICLLN 102

Query: 167 LSFKIVSNTVIIKVLFTLSFLLPRNTGIQLVNLFLL--------TLNDIYAKVTNEVI 18
           +SFKI++  ++ ++   +++++ +N    L N F++         LN ++ K ++ ++
Sbjct: 103 VSFKIITKVLMNRLDRIMTYIISKNQTAFLKNRFIMEGIVILHELLNSLHTKKSSGIL 160

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: 575,080,889
Number of extensions: 10092620
Number of successful extensions: 29801
Number of sequences better than 10.0: 10
Number of HSP's gapped: 29768
Number of HSP's successfully gapped: 10
Length of query: 152
Length of database: 1,040,966,779
Length adjustment: 114
Effective length of query: 38
Effective length of database: 675,678,289
Effective search space: 25675774982
Effective search space used: 25675774982
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: 0.75  gvh: 0.41  alm: 0.30  top: 0.57  tms: 0.07  mit: 0.50  mip: 0.07
 nuc: 0.06  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: 1.00  tyr: 0.51  leu: 0.13  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 

	 48.0 %: nuclear
	 28.0 %: cytoplasmic
	  8.0 %: Golgi
	  8.0 %: mitochondrial
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U06785-1 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