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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-U06849-1
Contig ID Contig-U06849-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06849-1 (Contig-U06849-1Q) /CSM_Contig/Contig-U06849-1Q.Seq.d
CTCTTATATATGCAATCTTTAATTGACTCAAAGGTTGATTTCATACCTAA
ATTTGATAATTTAATGTTATTTAATGATGCTGATGCTGATAATGATAATT
ATAATAATAATAATAATAATAATAAAACAAAAACAACCAATAACGATAAC
ACAATAAACACTTTAGAAATTGAAAAATTATTATCATCATTCACTTTATC
TAAAAGATTAAATATAGATGATCATTATCTTAGTGGAGTTAAATTACCAA
ACCCAAGTAATATTGTACATTTAAAAAGAAAATCAAATAAACATTTAGTA
TCAGCAGAATCTGTAAATAAACAACAACAACAACAACAACCACAACCACA
ACATGAACAAATTAAACAACAAAAAACAATTTCAAATACTCAAACCAATA
CCATCATTAATAAAGATAACGAAGAGATTACATTATCACCAATAGTAAAA
GATACAGCAGATAAAGCACCAATTGATAATGGAAATGTTACAAGTGATAA
TT
Gap no gap
Contig length 502
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 1046675
End point 1046173
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U06849
List of clone(s) 

est1=VSH234F,1,503
Translated Amino Acid sequence 
LLYMQSLIDSKVDFIPKFDNLMLFNDADADNDNYNNNNNNNKTKTTNNDNTINTLEIEKL
LSSFTLSKRLNIDDHYLSGVKLPNPSNIVHLKRKSNKHLVSAESVNKQQQQQQPQPQHEQ
IKQQKTISNTQTNTIINKDNEEITLSPIVKDTADKAPIDNGNVTSDN
Translated Amino Acid sequence (All Frames) 
Frame A:
LLYMQSLIDSKVDFIPKFDNLMLFNDADADNDNYNNNNNNNKTKTTNNDNTINTLEIEKL
LSSFTLSKRLNIDDHYLSGVKLPNPSNIVHLKRKSNKHLVSAESVNKQQQQQQPQPQHEQ
IKQQKTISNTQTNTIINKDNEEITLSPIVKDTADKAPIDNGNVTSDN


Frame B:
syicnl*ltqrlisylnlii*cylmmlmlimiiiiiiiiiikqkqpititq*tl*klkny
yhhslylkd*i*miiilvelnyqtqvilyi*kenqini*yqqnl*innnnnnnhnhnmnk
lnnkkqfqilkpipslikitkrlhyhq**kiqqikhqlimemlqvii


Frame C:
liyaifn*lkg*fht*i**fnvi**c*c****l********nknnq*r*hnkhfrn*kii
iiihfi*kikyr*sls*ws*itkpk*yctfkkkik*tfsisrick*ttttttttttt*tn
*ttknnfkysnqyhh**r*rrdyiitnskrysr*stn**wkcyk**
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06849-1 (Contig-U06849-1Q)
/CSM_Contig/Contig-U06849-1Q.Seq.d
         (502 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06849-1 (Contig-U06849-1Q) /CSM_Contig/Conti...   383  e-106
Contig-U12261-1 (Contig-U12261-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U10713-1 (Contig-U10713-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U10340-1 (Contig-U10340-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U13120-1 (Contig-U13120-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U04927-1 (Contig-U04927-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U14255-1 (Contig-U14255-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U13892-1 (Contig-U13892-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U13498-1 (Contig-U13498-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U13008-1 (Contig-U13008-1Q) /CSM_Contig/Conti...    34  0.14

>Contig-U06849-1 (Contig-U06849-1Q) /CSM_Contig/Contig-U06849-1Q.Seq.d
          Length = 502

 Score =  383 bits (193), Expect = e-106
 Identities = 193/193 (100%)
 Strand = Plus / Plus

                                                                       
Query: 126 aacaaaaacaaccaataacgataacacaataaacactttagaaattgaaaaattattatc 185
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 126 aacaaaaacaaccaataacgataacacaataaacactttagaaattgaaaaattattatc 185

                                                                       
Query: 186 atcattcactttatctaaaagattaaatatagatgatcattatcttagtggagttaaatt 245
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 186 atcattcactttatctaaaagattaaatatagatgatcattatcttagtggagttaaatt 245

                                                                       
Query: 246 accaaacccaagtaatattgtacatttaaaaagaaaatcaaataaacatttagtatcagc 305
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 246 accaaacccaagtaatattgtacatttaaaaagaaaatcaaataaacatttagtatcagc 305

                        
Query: 306 agaatctgtaaat 318
           |||||||||||||
Sbjct: 306 agaatctgtaaat 318


 Score =  244 bits (123), Expect = 8e-65
 Identities = 123/123 (100%)
 Strand = Plus / Plus

                                                                       
Query: 380 tttcaaatactcaaaccaataccatcattaataaagataacgaagagattacattatcac 439
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 380 tttcaaatactcaaaccaataccatcattaataaagataacgaagagattacattatcac 439

                                                                       
Query: 440 caatagtaaaagatacagcagataaagcaccaattgataatggaaatgttacaagtgata 499
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 440 caatagtaaaagatacagcagataaagcaccaattgataatggaaatgttacaagtgata 499

              
Query: 500 att 502
           |||
Sbjct: 500 att 502


 Score =  174 bits (88), Expect = 6e-44
 Identities = 88/88 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  ctcttatatatgcaatctttaattgactcaaaggttgatttcatacctaaatttgataat 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  ctcttatatatgcaatctttaattgactcaaaggttgatttcatacctaaatttgataat 60

                                      
Query: 61 ttaatgttatttaatgatgctgatgctg 88
          ||||||||||||||||||||||||||||
Sbjct: 61 ttaatgttatttaatgatgctgatgctg 88


>Contig-U12261-1 (Contig-U12261-1Q) /CSM_Contig/Contig-U12261-1Q.Seq.d
          Length = 1193

 Score = 38.2 bits (19), Expect = 0.009
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 165 agaaattgaaaaattatta 183
           |||||||||||||||||||
Sbjct: 493 agaaattgaaaaattatta 511


>Contig-U10713-1 (Contig-U10713-1Q) /CSM_Contig/Contig-U10713-1Q.Seq.d
          Length = 2682

 Score = 38.2 bits (19), Expect = 0.009
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 269 atttaaaaagaaaatcaaa 287
           |||||||||||||||||||
Sbjct: 671 atttaaaaagaaaatcaaa 689


  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: 9443
Number of Sequences: 6905
Number of extensions: 9443
Number of successful extensions: 1217
Number of sequences better than 10.0: 443
length of query: 502
length of database: 5,674,871
effective HSP length: 16
effective length of query: 486
effective length of database: 5,564,391
effective search space: 2704294026
effective search space used: 2704294026
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 2008.11.10
Homology vs DNA 
Query= Contig-U06849-1 (Contig-U06849-1Q) /CSM_Contig/Contig-U06849-1Q.Seq.d
         (502 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

(AU267113) Dictyostelium discoideum vegetative cDNA clone:VS...   278   e-145  3
(U66909) Dictyostelium discoideum ORF DG1003 gene, complete ...   204   e-135  4
(AC103223) Rattus norvegicus clone CH230-50N22, *** SEQUENCI...    34   0.17   2
(AC107538) Rattus norvegicus clone CH230-213H15, *** SEQUENC...    34   0.17   2
(FH337915) CHO_OF4598xn21r1.ab1 CHO_OF4 Nicotiana tabacum ge...    38   0.23   2
(FH255395) CHO_OF3009xk03r1.ab1 CHO_OF3 Nicotiana tabacum ge...    38   0.23   2
(DH174973) Oryzias latipes Fosmid clone:GOLWFno452_d15, reve...    48   0.30   1
(EC313530) REPROTRACTF081141F16 POSSUM_01-POSSUM-C-REPROTRAC...    48   0.30   1
(CV122055) Mdlv4001i09.y1 Mdlv Malus x domestica cDNA clone ...    48   0.30   1
(FD486861) rhgdcb0_000358.y1.scf cDNA Library of Trichoderma...    48   0.30   1
(CR931937) Zebrafish DNA sequence from clone DKEY-220O5.           46   1.2    1
(AU027238) Rattus norvegicus, OTSUKA clone, OT68.06/886f10, ...    46   1.2    1
(AC146077) Pan troglodytes BAC clone RP43-45A15 from chromos...    46   1.2    1
(AP008209) Oryza sativa (japonica cultivar-group) genomic DN...    46   1.2    1
(AC225524) Medicago truncatula clone mth2-13d9, complete seq...    46   1.2    1
(AC138199) Medicago truncatula chromosome 6 clone mth2-15g10...    46   1.2    1
(AC079853) Oryza sativa Japonica Group chromosome 3 clone OS...    46   1.2    1
(EA333227) Sequence 5719 from patent US 7306913.                   46   1.2    1
(DD315573) Primary Rat Hepatocyte Toxicity Modeling.               46   1.2    1
(AC073886) Homo sapiens BAC clone RP11-101N13 from 7, comple...    46   1.2    1
(AC151376) Callithrix jacchus clone CH259-271H10, WORKING DR...    46   1.2    1
(AC146240) Pan troglodytes chromosome UNK clone RP43-27L15, ...    46   1.2    1
(AC136820) Rattus norvegicus clone CH230-54I16, *** SEQUENCI...    46   1.2    1
(AC135520) Rattus norvegicus clone CH230-182B14, WORKING DRA...    46   1.2    1
(CU928000) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    46   1.2    1
(AC094015) Papio anubis clone RP41-382J16, WORKING DRAFT SEQ...    46   1.2    1
(AC093140) Pan troglodytes clone RP43-27L15, WORKING DRAFT S...    46   1.2    1
(AC210496) Oryza glaberrima clone OG_BBa0091N21, *** SEQUENC...    46   1.2    1
(AC165220) Medicago truncatula clone mth2-90e4, WORKING DRAF...    46   1.2    1
(FH182047) CHO_OF3085xd18f1.ab1 CHO_OF3 Nicotiana tabacum ge...    46   1.2    1
(DV719678) RVL10495 Wackym-Soares normalized rat vestibular ...    46   1.2    1
(CN543326) UI-R-DO1-cmj-n-17-0-UI.s1 UI-R-DO1 Rattus norvegi...    46   1.2    1
(CB611792) AMGNNUC:URRG1-00119-H8-A urrg1 (14046) Rattus nor...    46   1.2    1
(CA506870) UI-R-FJ0-cqc-l-01-0-UI.s1 UI-R-FJ0 Rattus norvegi...    46   1.2    1
(CA506266) UI-R-FJ0-cqa-p-22-0-UI.s1 UI-R-FJ0 Rattus norvegi...    46   1.2    1
(AI600031) EST251734 Normalized rat embryo, Bento Soares Rat...    46   1.2    1
(BQ191134) UI-R-DZ0-cmy-a-20-0-UI.s1 NCI_CGAP_DZ0 Rattus nor...    46   1.2    1
(AI179241) EST222932 Normalized rat spleen, Bento Soares Rat...    46   1.2    1
(AI176182) EST219763 Normalized rat ovary, Bento Soares Ratt...    46   1.2    1
(AI045752) UI-R-C1-kl-b-01-0-UI.s1 UI-R-C1 Rattus norvegicus...    46   1.2    1
(AI007927) EST202378 Normalized rat brain, Bento Soares Ratt...    46   1.2    1
(BI290101) UI-R-DK0-cfr-h-01-0-UI.s1 UI-R-DK0 Rattus norvegi...    46   1.2    1
(BI288223) UI-R-DK0-ccy-c-12-0-UI.s1 UI-R-DK0 Rattus norvegi...    46   1.2    1
(BF281863) EST446454 Rat Gene Index, normalized rat, Rattus ...    46   1.2    1
(AW914792) EST346096 Normalized rat ovary, Bento Soares Ratt...    46   1.2    1
(EI032804) hgz0009cd07.b1 hgz Oryza alta genomic clone hgz00...    42   1.7    2
(AC117189) Mus musculus BAC clone RP23-44D2 from 8, complete...    40   2.8    3
(AL928683) Mouse DNA sequence from clone RP23-78O17 on chrom...    42   4.1    2
(CR450755) Zebrafish DNA sequence from clone CH211-250G21 in...    44   4.7    1
(AL954362) Mouse DNA sequence from clone RP23-345L22 on chro...    44   4.7    1
(AM446835) Vitis vinifera, whole genome shotgun sequence, co...    44   4.7    1
(AC091857) Homo sapiens chromosome 5 clone CTD-2315L13, comp...    44   4.7    1
(AC018763) Homo sapiens chromosome 5 clone CTD-2305C23, comp...    44   4.7    1
(AC160503) Bos taurus clone CH240-85N3, WORKING DRAFT SEQUEN...    44   4.7    1
(AC098426) Rattus norvegicus clone CH230-2I22, *** SEQUENCIN...    44   4.7    1
(AC027149) Homo sapiens chromosome 18 clone RP11-94E2 map 18...    44   4.7    1
(AC201558) Strongylocentrotus purpuratus clone R3-3119L24, W...    44   4.7    1
(AC180829) Strongylocentrotus purpuratus clone R3-3071E19, W...    44   4.7    1
(AC178518) Strongylocentrotus purpuratus clone R3-3032B4, WO...    44   4.7    1
(ER602831) 1093016255411 Global-Ocean-Sampling_GS-36-01-01-2...    44   4.7    1
(ER352894) 1092347052228 Global-Ocean-Sampling_GS-34-01-01-1...    44   4.7    1
(EK201316) 1095460057486 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.7    1
(EJ505674) 1095403701950 Global-Ocean-Sampling_GS-28-01-01-1...    44   4.7    1
(DW273229) UI-S-GS1-acr-p-11-0-UI.s1 UI-S-GS1 Euprymna scolo...    44   4.7    1
(DR393671) USDA-FP_153604 Adult Alate Aphis gossypii (WHAGA)...    44   4.7    1
(FD381772) CeSi_F3_T7_C12_092 Ceratonia siliqua flowers cDNA...    44   4.7    1
(CP000061) Aster yellows witches'-broom phytoplasma AYWB, co...    44   4.7    1
(AP006628) Onion yellows phytoplasma OY-M DNA, complete genome.    44   4.7    1
(AL928916) Mouse DNA sequence *** SEQUENCING CANCELLED *** f...    42   5.1    2
(AC156710) Bos taurus clone CH240-57C10, WORKING DRAFT SEQUE...    38   5.4    4
(AC102812) Mus musculus clone RP23-75P2, *** SEQUENCING IN P...    42   5.5    2
(AC127857) Rattus norvegicus clone CH230-157E21, WORKING DRA...    38   5.8    2
(DX105358) MUGQ_CH252P019F22T7_GL331_091 CHORI-252 Vervet Mo...    38   6.0    2
(AC019170) Homo sapiens BAC clone RP11-162G9 from 4, complet...    32   8.5    2
(AC146414) Pan troglodytes chromosome UNK clone RP43-36G10, ...    38   8.5    3
(AC080125) Homo sapiens BAC clone RP11-175O15 from 2, comple...    36   9.7    3
(AC174287) Medicago truncatula clone mth2-32a8, complete seq...    34   9.9    4

>(AU267113) Dictyostelium discoideum vegetative cDNA clone:VSH234,
           5' end single read.
          Length = 503

 Score =  278 bits (140), Expect(3) = e-145
 Identities = 140/140 (100%)
 Strand = Plus / Plus


Query: 179 tattatcatcattcactttatctaaaagattaaatatagatgatcattatcttagtggag 238
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179 tattatcatcattcactttatctaaaagattaaatatagatgatcattatcttagtggag 238


Query: 239 ttaaattaccaaacccaagtaatattgtacatttaaaaagaaaatcaaataaacatttag 298
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 239 ttaaattaccaaacccaagtaatattgtacatttaaaaagaaaatcaaataaacatttag 298


Query: 299 tatcagcagaatctgtaaat 318
           ||||||||||||||||||||
Sbjct: 299 tatcagcagaatctgtaaat 318

 Score =  204 bits (103), Expect(3) = e-145
 Identities = 103/103 (100%)
 Strand = Plus / Plus


Query: 400 accatcattaataaagataacgaagagattacattatcaccaatagtaaaagatacagca 459
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 400 accatcattaataaagataacgaagagattacattatcaccaatagtaaaagatacagca 459


Query: 460 gataaagcaccaattgataatggaaatgttacaagtgataatt 502
           |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 460 gataaagcaccaattgataatggaaatgttacaagtgataatt 502

 Score = 93.7 bits (47), Expect(3) = e-145
 Identities = 47/47 (100%)
 Strand = Plus / Plus


Query: 1  ctcttatatatgcaatctttaattgactcaaaggttgatttcatacc 47
          |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  ctcttatatatgcaatctttaattgactcaaaggttgatttcatacc 47

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 364,900,651
Number of extensions: 22957724
Number of successful extensions: 2167256
Number of sequences better than 10.0: 77
Length of query: 502
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 479
Effective length of database: 93,106,754,628
Effective search space: 44598135466812
Effective search space used: 44598135466812
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.23
Homology vs Protein 
Query= Contig-U06849-1 (Contig-U06849-1Q) /CSM_Contig/Contig-U06849-1Q.Seq.d
         (502 letters)

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

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

 ***** No hits found ******

Lambda     K      H
   0.314    0.133    0.362

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: 460,956,116
Number of extensions: 5915952
Number of successful extensions: 8595
Number of sequences better than 10.0: 0
Number of HSP's gapped: 8592
Number of HSP's successfully gapped: 0
Length of query: 167
Length of database: 1,040,966,779
Length adjustment: 119
Effective length of query: 48
Effective length of database: 659,656,864
Effective search space: 31663529472
Effective search space used: 31663529472
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 30 (16.2 bits)
PSORT 

 psg: 0.61  gvh: 0.43  alm: 0.53  top: 0.53  tms: 0.00  mit: 0.19  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.33  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 

	 36.0 %: cytoplasmic
	 36.0 %: nuclear
	 12.0 %: mitochondrial
	  8.0 %: vacuolar
	  4.0 %: cytoskeletal
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U06849-1 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