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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-U13032-1
Contig ID Contig-U13032-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13032-1 (Contig-U13032-1Q) /CSM_Contig/Contig-U13032-1Q.Seq.d
TTAAATGCTAGTAAATCACCAAATGGTACATTAACAACTAGACCAGCAGC
AAAACTTGGTGCACCAGTTGATATTCAAGTATCATCACCAAAAGCACCAA
CACCAATACCAACATTATCATCACCATCACCATCACAATCAGCAGCACCA
CAACCAGCAGCACCACAACCAACACCAACATCACAACCACAACCACCAAC
AACAACAGTATCGACACCTGTATCACCAACATCCAAAGATTCAGATCAAT
TATTAGATGATATGATTTCACATTTTAAAGAGAGTAATTCAAATCTATTA
ACATCTTCAAGTAATCTTGACCCATCAGCTCCAAAAGTTGTTTATACATC
ACAACAATTCTATCCATTATCAGTTGAAGAACAATCATTACAATCAAAAG
TAAAAGTACAATTAACACCTGATGAACAAGTTATTCAAAAGATTTTAGGT
AATAATGATTTAGATGATGATATTACAAATAAAAATAATGATAATAATAG
CAATGGTAATAATAATAATAAAGAATTAATTGATGAACAGAATCAAATTG
AACAACAACAATCAGATAAATCATGGTATATTAAAGCACNNNNNNNNN
Gap no gap
Contig length 598
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 2950060
End point 2949472
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U13032
List of clone(s) 

est1=CHJ427F,1,589
Translated Amino Acid sequence 
LNASKSPNGTLTTRPAAKLGAPVDIQVSSPKAPTPIPTLSSPSPSQSAAPQPAAPQPTPT
SQPQPPTTTVSTPVSPTSKDSDQLLDDMISHFKESNSNLLTSSSNLDPSAPKVVYTSQQF
YPLSVEEQSLQSKVKVQLTPDEQVIQKILGNNDLDDDITNKNNDNNSNGNNNNKELIDEQ
NQIEQQQSDKSWYIKAXXX
Translated Amino Acid sequence (All Frames) 
Frame A:
LNASKSPNGTLTTRPAAKLGAPVDIQVSSPKAPTPIPTLSSPSPSQSAAPQPAAPQPTPT
SQPQPPTTTVSTPVSPTSKDSDQLLDDMISHFKESNSNLLTSSSNLDPSAPKVVYTSQQF
YPLSVEEQSLQSKVKVQLTPDEQVIQKILGNNDLDDDITNKNNDNNSNGNNNNKELIDEQ
NQIEQQQSDKSWYIKAXXX


Frame B:
*mlvnhqmvh*qldqqqnlvhqlifkyhhqkhqhqyqhyhhhhhhnqqhhnqqhhnqhqh
hnhnhqqqqyrhlyhqhpkiqiny*mi*fhilkrviqiy*hlqvilthqlqklfihhnns
ihyqlknnhynqk*kyn*hlmnklfkrf*vimi*mmilqikimiiiamviiiikn*lmnr
iklnnnnqinhgilkhxxx


Frame C:
kc**itkwyinn*tssktwcts*yssiitkstntntniiitititisstttsstttntni
tttttnnnsidtcitniqrfrsiir*ydftf*re*fksinifk*s*pissksclyittil
siis*rtiitikskstint**tsyskdfr***fr**yyk*k*****qw*****rin**te
sn*tttir*imvy*stxx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13032-1 (Contig-U13032-1Q)
/CSM_Contig/Contig-U13032-1Q.Seq.d
         (598 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13032-1 (Contig-U13032-1Q) /CSM_Contig/Conti...   478  e-135
Contig-U12177-1 (Contig-U12177-1Q) /CSM_Contig/Conti...    42  7e-04
Contig-U11332-1 (Contig-U11332-1Q) /CSM_Contig/Conti...    42  7e-04
Contig-U14772-1 (Contig-U14772-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U11757-1 (Contig-U11757-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U09732-1 (Contig-U09732-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U01481-1 (Contig-U01481-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U12500-1 (Contig-U12500-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U12188-1 (Contig-U12188-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U12124-1 (Contig-U12124-1Q) /CSM_Contig/Conti...    36  0.042

>Contig-U13032-1 (Contig-U13032-1Q) /CSM_Contig/Contig-U13032-1Q.Seq.d
          Length = 598

 Score =  478 bits (241), Expect = e-135
 Identities = 241/241 (100%)
 Strand = Plus / Plus

                                                                       
Query: 208 gtatcgacacctgtatcaccaacatccaaagattcagatcaattattagatgatatgatt 267
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 208 gtatcgacacctgtatcaccaacatccaaagattcagatcaattattagatgatatgatt 267

                                                                       
Query: 268 tcacattttaaagagagtaattcaaatctattaacatcttcaagtaatcttgacccatca 327
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 268 tcacattttaaagagagtaattcaaatctattaacatcttcaagtaatcttgacccatca 327

                                                                       
Query: 328 gctccaaaagttgtttatacatcacaacaattctatccattatcagttgaagaacaatca 387
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 328 gctccaaaagttgtttatacatcacaacaattctatccattatcagttgaagaacaatca 387

                                                                       
Query: 388 ttacaatcaaaagtaaaagtacaattaacacctgatgaacaagttattcaaaagatttta 447
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 388 ttacaatcaaaagtaaaagtacaattaacacctgatgaacaagttattcaaaagatttta 447

            
Query: 448 g 448
           |
Sbjct: 448 g 448


 Score =  254 bits (128), Expect = 1e-67
 Identities = 128/128 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ttaaatgctagtaaatcaccaaatggtacattaacaactagaccagcagcaaaacttggt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ttaaatgctagtaaatcaccaaatggtacattaacaactagaccagcagcaaaacttggt 60

                                                                       
Query: 61  gcaccagttgatattcaagtatcatcaccaaaagcaccaacaccaataccaacattatca 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gcaccagttgatattcaagtatcatcaccaaaagcaccaacaccaataccaacattatca 120

                   
Query: 121 tcaccatc 128
           ||||||||
Sbjct: 121 tcaccatc 128


 Score =  117 bits (59), Expect = 1e-26
 Identities = 59/59 (100%)
 Strand = Plus / Plus

                                                                      
Query: 531 tgatgaacagaatcaaattgaacaacaacaatcagataaatcatggtatattaaagcac 589
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 531 tgatgaacagaatcaaattgaacaacaacaatcagataaatcatggtatattaaagcac 589


>Contig-U12177-1 (Contig-U12177-1Q) /CSM_Contig/Contig-U12177-1Q.Seq.d
          Length = 630

 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 95  caccaacaccaataccaacat 115
           |||||||||||||||||||||
Sbjct: 300 caccaacaccaataccaacat 320


>Contig-U11332-1 (Contig-U11332-1Q) /CSM_Contig/Contig-U11332-1Q.Seq.d
          Length = 3658

 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                 
Query: 95   caccaacaccaataccaacat 115
            |||||||||||||||||||||
Sbjct: 1710 caccaacaccaataccaacat 1730


 Score = 32.2 bits (16), Expect = 0.65
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                                
Query: 93   agcaccaacaccaataccaa 112
            |||||||||||||| |||||
Sbjct: 1702 agcaccaacaccaacaccaa 1721


  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: 12,403
Number of Sequences: 6905
Number of extensions: 12403
Number of successful extensions: 1062
Number of sequences better than 10.0: 136
length of query: 598
length of database: 5,674,871
effective HSP length: 16
effective length of query: 582
effective length of database: 5,564,391
effective search space: 3238475562
effective search space used: 3238475562
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 2008.12. 5
Homology vs DNA 
Query= Contig-U13032-1 (Contig-U13032-1Q) /CSM_Contig/Contig-U13032-1Q.Seq.d
         (598 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

(BJ366803) Dictyostelium discoideum cDNA clone:ddc40f08, 5' ...   422   0.0    3
(AM485264) Vitis vinifera, whole genome shotgun sequence, co...    32   0.86   2
(CU571330) Zebrafish DNA sequence from clone CH73-38P6 in li...    46   1.4    1
(BV218098) S233P6145RA7.T0 LabradorRetriever Canis familiari...    46   1.4    1
(CU329670) Schizosaccharomyces pombe chromosome I.                 46   1.4    1
(AY460335) Nicotiana attenuata nitrate reductase mRNA, parti...    46   1.4    1
(CU928743) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   1.4    1
(ED477313) AUAC-aat02b07.b1 Ascaris suum whole genome shotgu...    34   3.7    2
(ED109980) AUAC-aac14h06.b1 Ascaris suum whole genome shotgu...    34   3.7    2
(AC220746) Bos taurus clone CH240-347O20, WORKING DRAFT SEQU...    42   4.5    3
(AY577213) Simian immunodeficiency virus clone H44.3 envelop...    44   5.7    1
(CU571240) M.truncatula DNA sequence from clone MTH2-54P7 on...    44   5.7    1
(AM457292) Vitis vinifera contig VV78X249912.5, whole genome...    44   5.7    1
(AM424379) Vitis vinifera contig VV78X093072.2, whole genome...    44   5.7    1
(AC131621) Rattus norvegicus clone CH230-160H17, *** SEQUENC...    44   5.7    1
(ET626640) fcg3x.308950h22.f C. graminicola genomic sequence...    44   5.7    1
(ET599857) fcg3x.225850l21 C. graminicola genomic sequence G...    44   5.7    1
(ET561259) fcg3x.231550l13 C. graminicola genomic sequence G...    44   5.7    1
(ET546252) fcg3x.223650o03 C. graminicola genomic sequence G...    44   5.7    1
(ET387857) S0054J22_T7 CHORI-214 Salmo salar genomic clone S...    44   5.7    1
(ET384749) S0227G07_T7 CHORI-214 Salmo salar genomic clone S...    44   5.7    1
(ET111002) QM0AAC19DE09FM1 CCH3 Citrus clementina genomic cl...    44   5.7    1
(ER966291) SOOAT81JR LargeInsertSoybeanGenLibBuild4 Glycine ...    44   5.7    1
(EI351303) GM_WBc0100A19.f GM_WBc Glycine max genomic clone ...    44   5.7    1
(EI322186) GM_WBc0057O22.f GM_WBc Glycine max genomic clone ...    44   5.7    1
(EI317699) GM_WBc0051K08.f GM_WBc Glycine max genomic clone ...    44   5.7    1
(ED660645) GM_WBa0083A11.f GM_WBa Glycine max genomic clone ...    44   5.7    1
(CT522650) A BAC library has been constructed from cultivar ...    44   5.7    1
(CR334266) mte1-64H21FM2 BAC end, cultivar Jemalong A17 of M...    44   5.7    1
(CR308535) mte1-3G1FM1 BAC end, cultivar Jemalong A17 of Med...    44   5.7    1
(CX526652) s13dNF25B11AT093_513816 Aphid-Infected Shoots Med...    44   5.7    1
(CX526072) s13dNF33H10AT092_509888 Aphid-Infected Shoots Med...    44   5.7    1
(CV795873) UI-R-CN1-cmo-i-07-0-UI.s1 UI-R-CN1 Rattus norvegi...    44   5.7    1
(CT764989) Paramecium tetraurelia 5-PRIME EST from clone LK0...    44   5.7    1
(BI263964) NF111E02PL1F1019 Phosphate starved leaf Medicago ...    44   5.7    1
(BG447573) NF118A12ST1F1088 Developing stem Medicago truncat...    44   5.7    1
(AW697338) NF115F04ST1F1042 Developing stem Medicago truncat...    44   5.7    1
(EU723844) Wolbachia endosymbiont of Propylea japonica outer...    44   5.7    1
(EF502046) Wolbachia endosymbiont of Coccinella undecimpunct...    44   5.7    1
(BA000026) Mycoplasma penetrans HF-2 DNA, complete genome.         44   5.7    1
(AJ276607) Wolbachia endosymbiont of Porcellio scaber partia...    44   5.7    1
(AJ269476) Wolbachia sp. sWca partial wsp gene for outer sur...    44   5.7    1
(AJ130715) Wolbachia sp. (Adalia bipunctata host, strain Z) ...    44   5.7    1
(AF539861) Wolbachia endosymbiont of Aphthona nigriscutis cl...    44   5.7    1
(AF539860) Wolbachia endosymbiont of Aphthona nigriscutis cl...    44   5.7    1
(AF481168) Wolbachia pipientis isolate wCoaR outer surface p...    44   5.7    1
(AF217724) Wolbachia sp. wFus-B1 outer surface protein precu...    44   5.7    1
(AB109594) Wolbachia endosymbiont of Scotinophara lurida (st...    44   5.7    1
(AB037893) Wolbachia sp. wNaw wsp gene for outer surface pro...    44   5.7    1
(CU812591) A BAC library has been constructed from PN40024 g...    40   6.1    2
(AP008207) Oryza sativa (japonica cultivar-group) genomic DN...    32   6.4    2
(AC121370) Rattus norvegicus clone CH230-161D16, *** SEQUENC...    30   10.0   2

>(BJ366803) Dictyostelium discoideum cDNA clone:ddc40f08, 5' end,
           single read.
          Length = 589

 Score =  422 bits (213), Expect(3) = 0.0
 Identities = 213/213 (100%)
 Strand = Plus / Plus


Query: 237 agattcagatcaattattagatgatatgatttcacattttaaagagagtaattcaaatct 296
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237 agattcagatcaattattagatgatatgatttcacattttaaagagagtaattcaaatct 296


Query: 297 attaacatcttcaagtaatcttgacccatcagctccaaaagttgtttatacatcacaaca 356
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 297 attaacatcttcaagtaatcttgacccatcagctccaaaagttgtttatacatcacaaca 356


Query: 357 attctatccattatcagttgaagaacaatcattacaatcaaaagtaaaagtacaattaac 416
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 357 attctatccattatcagttgaagaacaatcattacaatcaaaagtaaaagtacaattaac 416


Query: 417 acctgatgaacaagttattcaaaagattttagg 449
           |||||||||||||||||||||||||||||||||
Sbjct: 417 acctgatgaacaagttattcaaaagattttagg 449

 Score =  230 bits (116), Expect(3) = 0.0
 Identities = 116/116 (100%)
 Strand = Plus / Plus


Query: 1   ttaaatgctagtaaatcaccaaatggtacattaacaactagaccagcagcaaaacttggt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ttaaatgctagtaaatcaccaaatggtacattaacaactagaccagcagcaaaacttggt 60


Query: 61  gcaccagttgatattcaagtatcatcaccaaaagcaccaacaccaataccaacatt 116
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gcaccagttgatattcaagtatcatcaccaaaagcaccaacaccaataccaacatt 116

 Score =  117 bits (59), Expect(3) = 0.0
 Identities = 59/59 (100%)
 Strand = Plus / Plus


Query: 531 tgatgaacagaatcaaattgaacaacaacaatcagataaatcatggtatattaaagcac 589
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 531 tgatgaacagaatcaaattgaacaacaacaatcagataaatcatggtatattaaagcac 589

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 446,790,067
Number of extensions: 28930449
Number of successful extensions: 2056936
Number of sequences better than 10.0: 53
Length of query: 598
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 575
Effective length of database: 93,106,754,628
Effective search space: 53536383911100
Effective search space used: 53536383911100
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7. 5
Homology vs Protein 
Query= Contig-U13032-1 (Contig-U13032-1Q) /CSM_Contig/Contig-U13032-1Q.Seq.d
         (598 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54VU5) RecName: Full=Probable inactive serine/threonine-protei...   194   2e-48
(Q54KF7) RecName: Full=Integrin beta-like protein A; AltName: Fu...    33   7.8

>(Q54VU5) RecName: Full=Probable inactive serine/threonine-protein
           kinase DDB_G0280131;
          Length = 1192

 Score =  194 bits (492), Expect = 2e-48
 Identities = 114/196 (58%), Positives = 114/196 (58%)
 Frame = +1

Query: 1   LNASKSPNGTLTTRPAAKLGAPVDIQVSSPKXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 180
           LNASKSPNGTLTTRPAAKLGAPVDIQVSSPK
Sbjct: 326 LNASKSPNGTLTTRPAAKLGAPVDIQVSSPKAPTPIPTLSSPSPSQSAAPQPAAPQPTPT 385

Query: 181 XXXXXXXXXXXXXXXXXXKDSDQLLDDMISHFKEXXXXXXXXXXXXDPSAPKVVYTSQQF 360
                             KDSDQLLDDMISHFKE            DPSAPKVVYTSQQF
Sbjct: 386 SQPQPPTTTVSTPVSPTFKDSDQLLDDMISHFKESNSNLLTSSSNLDPSAPKVVYTSQQF 445

Query: 361 YPLSVEEQSLQSKVKVQLTPDEQVIQKILGXXXXXXXXXXXXXXXXXXXXXXXKELIDEQ 540
           YPLSVEEQSLQSKVKVQLTPDEQVIQKILG                       KELIDEQ
Sbjct: 446 YPLSVEEQSLQSKVKVQLTPDEQVIQKILGNNDLDDDITNKNNDNNSNGNNNNKELIDEQ 505

Query: 541 NQIEQQQSDKSWYIKA 588
           NQIEQQQSDKSWYIKA
Sbjct: 506 NQIEQQQSDKSWYIKA 521

Lambda     K      H
   0.307    0.125    0.336

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: 402,771,771
Number of extensions: 4535195
Number of successful extensions: 9251
Number of sequences better than 10.0: 2
Number of HSP's gapped: 9244
Number of HSP's successfully gapped: 3
Length of query: 199
Length of database: 1,051,180,864
Length adjustment: 122
Effective length of query: 77
Effective length of database: 656,320,666
Effective search space: 50536691282
Effective search space used: 50536691282
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.2 bits)
S2: 30 (16.2 bits)
PSORT 

 psg: 0.79  gvh: 0.53  alm: 0.55  top: 0.53  tms: 0.00  mit: 0.31  mip: 0.04
 nuc: 0.00  erl: 0.00  erm: 0.20  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 %: nuclear
	 24.0 %: mitochondrial
	 20.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for Contig-U13032-1 is nuc
VS (DIR, S) 0
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) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0