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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-U06290-1
Contig ID Contig-U06290-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06290-1 (Contig-U06290-1Q) /CSM_Contig/Contig-U06290-1Q.Seq.d
CATTACCAGATCTTTATCCATACATATTACCATTATCAGATAATAGTAGT
TTTTGGAATGCCTCTCAATTCATACCAGATGTGTTAGTTATTAATTTAGG
TTCAAATGATTATACAGATTTACCATACCCACCAAATGATTACTTTCAAG
TTAAATTTATTGAATTTGTAAAATCAATCATTATAAACTATAATCATCAA
ATTCCAAAGATTTTCTTTATATGTGGTGTAATGGTTAATGAACATCCATG
TTGTACAATTACTGAAGCTGTTTCAAATGTTTTCAATGCTACTTATATTG
ATATGCCAAATATTCAAAATTCAAGTGATGACTTTGGTTGTTATGGCCAT
CCAACTATAATTGCTCATGCTCATATGGCTTCAATTGCAATTCCAATTAT
AAAACAAGTAATGAATTGGGAATAAATAAATAAATAAACAAATAAATAAA
ATAAAATAAATAAAATAAATAAATAAATAAATAAATAAATAAATAAATAA
ATAAATAAATAAATATATTTTGTTTATTAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAA
Gap no gap
Contig length 561
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 5426020
End point 5426548
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U06290
List of clone(s) 

est1=VSA632Z,1,562
Translated Amino Acid sequence 
LPDLYPYILPLSDNSSFWNASQFIPDVLVINLGSNDYTDLPYPPNDYFQVKFIEFVKSII
INYNHQIPKIFFICGVMVNEHPCCTITEAVSNVFNATYIDMPNIQNSSDDFGCYGHPTII
AHAHMASIAIPIIKQVMNWE*ink*tnk*nkinkink*ink*ink*ink*iyfvy*kkkk
kkkkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
hyqifihtyyhyqiivvfgmplnsyqmc*lli*vqmiiqiyhthqmitfklnllnl*nqs
l*tiiikfqrfslyvv*wlmnihvvqllklfqmfsmllilicqifkiqvmtlvvmaiql*
llmliwlqlqfql*nk**ignk*inkqinkik*ik*ink*ink*ink*inkyilfikkkk
kkkkkkk


Frame B:
itrslsihitiir***fleclsihtrcvsy*frfk*lyrftiptk*llss*iy*ickinh
ykl*ssnskdflymwcng**tsmlyny*scfkcfqcyly*yakyskfk**lwllwpsnyn
cscsygfncnsnyktsnelgink*ink*ik*nk*nk*ink*ink*ink*inifcllkkkk
kkkkkk


Frame C:
LPDLYPYILPLSDNSSFWNASQFIPDVLVINLGSNDYTDLPYPPNDYFQVKFIEFVKSII
INYNHQIPKIFFICGVMVNEHPCCTITEAVSNVFNATYIDMPNIQNSSDDFGCYGHPTII
AHAHMASIAIPIIKQVMNWE*ink*tnk*nkinkink*ink*ink*ink*iyfvy*kkkk
kkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06290-1 (Contig-U06290-1Q)
/CSM_Contig/Contig-U06290-1Q.Seq.d
         (561 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06290-1 (Contig-U06290-1Q) /CSM_Contig/Conti...   833  0.0
Contig-U11862-1 (Contig-U11862-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U07099-1 (Contig-U07099-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U14650-1 (Contig-U14650-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U11673-1 (Contig-U11673-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U10772-1 (Contig-U10772-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U10456-1 (Contig-U10456-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U03858-1 (Contig-U03858-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U14402-1 (Contig-U14402-1Q) /CSM_Contig/Conti...    32  0.61
Contig-U09690-1 (Contig-U09690-1Q) /CSM_Contig/Conti...    28  9.5

>Contig-U06290-1 (Contig-U06290-1Q) /CSM_Contig/Contig-U06290-1Q.Seq.d
          Length = 561

 Score =  833 bits (420), Expect = 0.0
 Identities = 420/420 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   cattaccagatctttatccatacatattaccattatcagataatagtagtttttggaatg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   cattaccagatctttatccatacatattaccattatcagataatagtagtttttggaatg 60

                                                                       
Query: 61  cctctcaattcataccagatgtgttagttattaatttaggttcaaatgattatacagatt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  cctctcaattcataccagatgtgttagttattaatttaggttcaaatgattatacagatt 120

                                                                       
Query: 121 taccatacccaccaaatgattactttcaagttaaatttattgaatttgtaaaatcaatca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 taccatacccaccaaatgattactttcaagttaaatttattgaatttgtaaaatcaatca 180

                                                                       
Query: 181 ttataaactataatcatcaaattccaaagattttctttatatgtggtgtaatggttaatg 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ttataaactataatcatcaaattccaaagattttctttatatgtggtgtaatggttaatg 240

                                                                       
Query: 241 aacatccatgttgtacaattactgaagctgtttcaaatgttttcaatgctacttatattg 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aacatccatgttgtacaattactgaagctgtttcaaatgttttcaatgctacttatattg 300

                                                                       
Query: 301 atatgccaaatattcaaaattcaagtgatgactttggttgttatggccatccaactataa 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 atatgccaaatattcaaaattcaagtgatgactttggttgttatggccatccaactataa 360

                                                                       
Query: 361 ttgctcatgctcatatggcttcaattgcaattccaattataaaacaagtaatgaattggg 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 ttgctcatgctcatatggcttcaattgcaattccaattataaaacaagtaatgaattggg 420


 Score = 32.2 bits (16), Expect = 0.61
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 513 atatattttgtttatt 528
           ||||||||||||||||
Sbjct: 513 atatattttgtttatt 528


>Contig-U11862-1 (Contig-U11862-1Q) /CSM_Contig/Contig-U11862-1Q.Seq.d
          Length = 1881

 Score = 38.2 bits (19), Expect = 0.010
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                               
Query: 18   ccatacatattaccattat 36
            |||||||||||||||||||
Sbjct: 1131 ccatacatattaccattat 1113


>Contig-U07099-1 (Contig-U07099-1Q) /CSM_Contig/Contig-U07099-1Q.Seq.d
          Length = 169

 Score = 36.2 bits (18), Expect = 0.039
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 146 tcaagttaaatttattga 163
           ||||||||||||||||||
Sbjct: 102 tcaagttaaatttattga 119


  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: 6773
Number of Sequences: 6905
Number of extensions: 6773
Number of successful extensions: 701
Number of sequences better than 10.0: 226
length of query: 561
length of database: 5,674,871
effective HSP length: 16
effective length of query: 545
effective length of database: 5,564,391
effective search space: 3032593095
effective search space used: 3032593095
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. 8
Homology vs DNA 
Query= Contig-U06290-1 (Contig-U06290-1Q) /CSM_Contig/Contig-U06290-1Q.Seq.d
         (561 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

(AU261617) Dictyostelium discoideum vegetative cDNA clone:VS...   757   0.0    1
(ET696230) CHO_OF359xo21f1.ab1 CHO_OF Nicotiana tabacum geno...    50   0.086  1
(BX511269) Zebrafish DNA sequence from clone CH211-207N9 in ...    46   1.3    1
(AC127020) Medicago truncatula chromosome 6 clone mth2-9p1, ...    46   1.3    1
(AC108011) Homo sapiens BAC clone RP13-511O19 from 4, comple...    46   1.3    1
(DH100712) Oryzias latipes Fosmid clone:GOLWFno346_o19, forw...    46   1.3    1
(EJ361096) 1092963686764 Global-Ocean-Sampling_GS-28-01-01-1...    38   2.4    2
(CU468180) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    32   2.6    2
(BA000021) Wigglesworthia glossinidia endosymbiont of Glossi...    36   3.1    7
(AC090818) Homo sapiens chromosome 11 clone CTD-2041N13 map ...    36   4.0    5
(AC181463) Strongylocentrotus purpuratus clone R3-51D4, WORK...    44   4.7    2
(AC117176) Dictyostelium discoideum chromosome 2 map 5018074...    40   4.8    6
(AC224522) Bos taurus clone CH240-483G14, WORKING DRAFT SEQU...    44   5.3    1
(AC223619) Bos taurus clone CH240-463N2, WORKING DRAFT SEQUE...    44   5.3    1
(AC220658) Bos taurus clone CH240-351C17, WORKING DRAFT SEQU...    44   5.3    1
(AC201595) Strongylocentrotus purpuratus clone R3-42O1, WORK...    44   5.3    1
(AC201411) Strongylocentrotus purpuratus clone R3-17N24, WOR...    44   5.3    1
(AC201290) Strongylocentrotus purpuratus clone R3-16G19, WOR...    44   5.3    1
(AC201005) Strongylocentrotus purpuratus clone R3-12F20, WOR...    44   5.3    1
(AC184682) Strongylocentrotus purpuratus clone R3-3026B20, *...    44   5.3    1
(AC184563) Strongylocentrotus purpuratus clone R3-3110L10, W...    44   5.3    1
(AC184425) Strongylocentrotus purpuratus clone R3-3077M13, W...    44   5.3    1
(AC184331) Strongylocentrotus purpuratus clone R3-3037M7, WO...    44   5.3    1
(AC181921) Strongylocentrotus purpuratus clone R3-1009M20, W...    44   5.3    1
(AC181715) Strongylocentrotus purpuratus clone R3-1039I03, W...    44   5.3    1
(AC181077) Strongylocentrotus purpuratus clone R3-3047P02, W...    44   5.3    1
(AC180897) Strongylocentrotus purpuratus clone R3-3064E11, W...    44   5.3    1
(AC180855) Strongylocentrotus purpuratus clone R3-3069C1, WO...    44   5.3    1
(AC180489) Strongylocentrotus purpuratus clone R3-3100A18, W...    44   5.3    1
(AC180340) Strongylocentrotus purpuratus clone R3-3118N11, W...    44   5.3    1
(AC179795) Strongylocentrotus purpuratus clone R3-1014I4, WO...    44   5.3    1
(AC179384) Strongylocentrotus purpuratus clone R3-1101L15, W...    44   5.3    1
(AC179371) Strongylocentrotus purpuratus clone R3-59L9, WORK...    44   5.3    1
(AC179197) Strongylocentrotus purpuratus clone R3-4019G13, W...    44   5.3    1
(AC179170) Strongylocentrotus purpuratus clone R3-4016G24, W...    44   5.3    1
(AC179162) Strongylocentrotus purpuratus clone R3-4016A3, WO...    44   5.3    1
(AC179015) Strongylocentrotus purpuratus clone R3-32J24, WOR...    44   5.3    1
(AC177546) Strongylocentrotus purpuratus clone R3-1026N6, WO...    44   5.3    1
(AC177493) Strongylocentrotus purpuratus clone R3-1027N13, W...    44   5.3    1
(AC177151) Strongylocentrotus purpuratus clone R3-4015A11, W...    44   5.3    1
(AC177115) Strongylocentrotus purpuratus clone R3-4014C5, WO...    44   5.3    1
(AC176919) Strongylocentrotus purpuratus clone R3-1104K4, WO...    44   5.3    1
(AC176735) Strongylocentrotus purpuratus clone R3-3096O8, WO...    44   5.3    1
(AC176570) Strongylocentrotus purpuratus clone R3-3077A08, W...    44   5.3    1
(AC176289) Strongylocentrotus purpuratus clone R3-3057I2, WO...    44   5.3    1
(AC176181) Strongylocentrotus purpuratus clone R3-3066L19, W...    44   5.3    1
(AC175939) Strongylocentrotus purpuratus clone R3-17B13, WOR...    44   5.3    1
(AC175915) Strongylocentrotus purpuratus clone R3-12O21, WOR...    44   5.3    1
(AC175882) Strongylocentrotus purpuratus clone R3-15C9, WORK...    44   5.3    1
(AC175879) Strongylocentrotus purpuratus clone R3-15D21, WOR...    44   5.3    1
(AC175842) Strongylocentrotus purpuratus clone R3-15L24, WOR...    44   5.3    1
(CG820351) SOYAB32TH LargeInsertSoybeanGenLib Glycine max ge...    44   5.3    1
(CN576942) rc53d12.x1 Meloidogyne hapla egg pAMP1 v1 Meloido...    44   5.3    1
(CB282218) BT0188 Blomia tropicalis cDNA library Blomia trop...    44   5.3    1
(AM435574) Vitis vinifera contig VV78X185436.27, whole genom...    36   6.2    5
(BU569585) AGENCOURT_10359713 NIH_MGC_82 Homo sapiens cDNA c...    40   7.5    2
(CP000102) Methanosphaera stadtmanae DSM 3091, complete genome.    32   8.1    2
(AC161830) Bos taurus clone CH240-100A23, WORKING DRAFT SEQU...    32   9.4    2
(DD333453) A method of testing a sensitivity of tumor cells ...    32   9.8    2
(AL008730) Human DNA sequence from clone RP3-487J7 on chromo...    32   9.8    2
(EK314978) 1095462409965 Global-Ocean-Sampling_GS-31-01-01-1...    40   9.9    2

>(AU261617) Dictyostelium discoideum vegetative cDNA clone:VSA632,
           3' end single read.
          Length = 562

 Score =  757 bits (382), Expect = 0.0
 Identities = 382/382 (100%)
 Strand = Plus / Plus


Query: 1   cattaccagatctttatccatacatattaccattatcagataatagtagtttttggaatg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   cattaccagatctttatccatacatattaccattatcagataatagtagtttttggaatg 60


Query: 61  cctctcaattcataccagatgtgttagttattaatttaggttcaaatgattatacagatt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  cctctcaattcataccagatgtgttagttattaatttaggttcaaatgattatacagatt 120


Query: 121 taccatacccaccaaatgattactttcaagttaaatttattgaatttgtaaaatcaatca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 taccatacccaccaaatgattactttcaagttaaatttattgaatttgtaaaatcaatca 180


Query: 181 ttataaactataatcatcaaattccaaagattttctttatatgtggtgtaatggttaatg 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ttataaactataatcatcaaattccaaagattttctttatatgtggtgtaatggttaatg 240


Query: 241 aacatccatgttgtacaattactgaagctgtttcaaatgttttcaatgctacttatattg 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aacatccatgttgtacaattactgaagctgtttcaaatgttttcaatgctacttatattg 300


Query: 301 atatgccaaatattcaaaattcaagtgatgactttggttgttatggccatccaactataa 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 atatgccaaatattcaaaattcaagtgatgactttggttgttatggccatccaactataa 360


Query: 361 ttgctcatgctcatatggcttc 382
           ||||||||||||||||||||||
Sbjct: 361 ttgctcatgctcatatggcttc 382

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 465,260,723
Number of extensions: 27870945
Number of successful extensions: 2307513
Number of sequences better than 10.0: 63
Length of query: 561
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 538
Effective length of database: 93,106,754,628
Effective search space: 50091433989864
Effective search space used: 50091433989864
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 6.21
Homology vs Protein 
Query= Contig-U06290-1 (Contig-U06290-1Q) /CSM_Contig/Contig-U06290-1Q.Seq.d
         (561 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP000383_714(CP000383|pid:none) Cytophaga hutchinsonii ATCC 3340...    49   9e-05
A96966(A96966) hypothetical protein CAC0537 [imported] - Clostri...    46   8e-04
CP000885_1241(CP000885|pid:none) Clostridium phytofermentans ISD...    44   0.003
CP001348_2116(CP001348|pid:none) Clostridium cellulolyticum H10,...    41   0.024
AE015928_2621(AE015928|pid:none) Bacteroides thetaiotaomicron VP...    34   3.0
CP000153_1279(CP000153|pid:none) Sulfurimonas denitrificans DSM ...    33   5.1
AB065766_1(AB065766|pid:none) Homo sapiens gene for seven transm...    28   5.2
CP000061_561(CP000061|pid:none) Aster yellows witches'-broom phy...    32   8.8

>CP000383_714(CP000383|pid:none) Cytophaga hutchinsonii ATCC 33406,
           complete genome.
          Length = 387

 Score = 48.9 bits (115), Expect = 9e-05
 Identities = 34/85 (40%), Positives = 45/85 (52%), Gaps = 5/85 (5%)
 Frame = +3

Query: 3   LPDLYPYILPLSDNSSFWNASQFIPDVLVINLGSNDY--TDLPYPPND-YFQVKFIEFVK 173
           LP +Y  I     NS FW+ +  IPD++VINLG+NDY       P ND  F  ++I FV
Sbjct: 236 LPQIYDRIHLHDKNSLFWDHANQIPDIIVINLGTNDYFGESQNQPLNDTVFVHRYIAFVD 295

Query: 174 SIIINYNHQIPKIFFIC--GVMVNE 242
            +   Y    PK   IC  G M+N+
Sbjct: 296 RLSTYY----PKAQIICANGSMLND 316

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: 687,738,121
Number of extensions: 11520442
Number of successful extensions: 24632
Number of sequences better than 10.0: 8
Number of HSP's gapped: 24628
Number of HSP's successfully gapped: 9
Length of query: 187
Length of database: 1,040,966,779
Length adjustment: 121
Effective length of query: 66
Effective length of database: 653,248,294
Effective search space: 43114387404
Effective search space used: 43114387404
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: 30 (16.2 bits)
PSORT 

 psg: 0.75  gvh: 0.37  alm: 0.37  top: 0.53  tms: 0.00  mit: 0.20  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: 0.00  m3b: 0.00  m_ : 1.00 

	 60.0 %: cytoplasmic
	 28.0 %: nuclear
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U06290-1 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