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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-U06692-1
Contig ID Contig-U06692-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06692-1 (Contig-U06692-1Q) /CSM_Contig/Contig-U06692-1Q.Seq.d
ATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTAT
TTATTTATTCATTTATTTTATTTATTTATTTTATTTTATTTATTTATTCA
ATTTTTAATTTTATTTAAAAATATGGAAGAAATTCAACCATCATCATCAA
AAGAAACGGAATCTATTAATAGTAATGAAAATGATAATGATAATAAAATT
AGTACTACACCAGTTATTTCTATATCAACATTTATAAAGAGTAAAAAAAG
TGCATCAACAAGTACATCACCACCGAAATCTGGTTCATTATTATCAATTC
AAAGAACTTTAAAAAATAGTTCAGAAACACAAATTATAAAAGAAAAAAAG
TAATAATAAAAAAAATTTTAAAAAAAAA
Gap no gap
Contig length 378
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 6236055
End point 6236434
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 4
Link to clone list U06692
List of clone(s) 

est1=VSF305F,1,379
est2=VSF305Z,1,364
est3=VSF343F,1,379
est4=VSF343Z,1,355
Translated Amino Acid sequence 
LFIYLFIYLFIYLFIYLFIHLFYLFILFYLFIQFLILFKNMEEIQPSSSKETESINSNEN
DNDNKISTTPVISISTFIKSKKSASTSTSPPKSGSLLSIQRTLKNSSETQIIKEKK***k
kf*kk
Translated Amino Acid sequence (All Frames) 
Frame A:
iylfiylfiylfiylfiylfiyfiylfyfiylfnf*fylkiwkkfnhhhqkkrnllivmk
mimiiklvlhqlflyqhl*rvkkvhqqvhhhrnlvhyyqfkel*kivqkhkl*kkksnnk
knfkkk


Frame B:
fiylfiylfiylfiylfiysfilfiyfilfiysifnfi*kygrnstiiikrngiy****k
*****n*yytsyfyiniyke*kkcinkyitteiwfiiinsknfkk*frntnykrkkviik
kilkk


Frame C:
LFIYLFIYLFIYLFIYLFIHLFYLFILFYLFIQFLILFKNMEEIQPSSSKETESINSNEN
DNDNKISTTPVISISTFIKSKKSASTSTSPPKSGSLLSIQRTLKNSSETQIIKEKK***k
kf*kk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06692-1 (Contig-U06692-1Q)
/CSM_Contig/Contig-U06692-1Q.Seq.d
         (378 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06692-1 (Contig-U06692-1Q) /CSM_Contig/Conti...   381  e-106
Contig-U09374-1 (Contig-U09374-1Q) /CSM_Contig/Conti...    44  1e-04
Contig-U09327-1 (Contig-U09327-1Q) /CSM_Contig/Conti...    44  1e-04
Contig-U13810-1 (Contig-U13810-1Q) /CSM_Contig/Conti...    42  4e-04
Contig-U13880-1 (Contig-U13880-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U12260-1 (Contig-U12260-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U11796-1 (Contig-U11796-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U10790-1 (Contig-U10790-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U06778-1 (Contig-U06778-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U03678-1 (Contig-U03678-1Q) /CSM_Contig/Conti...    40  0.002

>Contig-U06692-1 (Contig-U06692-1Q) /CSM_Contig/Contig-U06692-1Q.Seq.d
          Length = 378

 Score =  381 bits (192), Expect = e-106
 Identities = 206/213 (96%)
 Strand = Plus / Plus

                                                                       
Query: 118 aaaatatggaagaaattcaaccatcatcatcaaaagaaacggaatctattaatagtaatg 177
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 118 aaaatatggaagaaattcaaccatcatcatcaaaagaaacggaatctattaatagtaatg 177

                                                                       
Query: 178 aaaatgataatgataataaaattagtactacaccagttatttctatatcaacatttataa 237
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 178 aaaatgataatgataataaaattagtactacaccagttatttctatatcaacatttataa 237

                                                                       
Query: 238 agagtnnnnnnngtgcatcaacaagtacatcaccaccgaaatctggttcattattatcaa 297
           |||||       ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238 agagtaaaaaaagtgcatcaacaagtacatcaccaccgaaatctggttcattattatcaa 297

                                            
Query: 298 ttcaaagaactttaaaaaatagttcagaaacac 330
           |||||||||||||||||||||||||||||||||
Sbjct: 298 ttcaaagaactttaaaaaatagttcagaaacac 330


>Contig-U09374-1 (Contig-U09374-1Q) /CSM_Contig/Contig-U09374-1Q.Seq.d
          Length = 1095

 Score = 44.1 bits (22), Expect = 1e-04
 Identities = 25/26 (96%)
 Strand = Plus / Plus

                                     
Query: 173 taatgaaaatgataatgataataaaa 198
           |||||| |||||||||||||||||||
Sbjct: 413 taatgataatgataatgataataaaa 438


>Contig-U09327-1 (Contig-U09327-1Q) /CSM_Contig/Contig-U09327-1Q.Seq.d
          Length = 534

 Score = 44.1 bits (22), Expect = 1e-04
 Identities = 28/30 (93%)
 Strand = Plus / Plus

                                         
Query: 167 taatagtaatgaaaatgataatgataataa 196
           |||||||||| | |||||||||||||||||
Sbjct: 352 taatagtaataataatgataatgataataa 381


  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: 7411
Number of Sequences: 6905
Number of extensions: 7411
Number of successful extensions: 1095
Number of sequences better than 10.0: 374
length of query: 378
length of database: 5,674,871
effective HSP length: 16
effective length of query: 362
effective length of database: 5,564,391
effective search space: 2014309542
effective search space used: 2014309542
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-U06692-1 (Contig-U06692-1Q) /CSM_Contig/Contig-U06692-1Q.Seq.d
         (378 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

(AC116979) Dictyostelium discoideum chromosome 2 map 6445720...   248   3e-91  2
(AU265083) Dictyostelium discoideum vegetative cDNA clone:VS...   248   3e-91  2
(AU265020) Dictyostelium discoideum vegetative cDNA clone:VS...   248   3e-91  2
(AU265021) Dictyostelium discoideum vegetative cDNA clone:VS...   248   3e-91  2
(AU265084) Dictyostelium discoideum vegetative cDNA clone:VS...   248   3e-91  2
(DH714852) Rattus norvegicus DNA, BAC clone: RNB1-279P14, 5'...    56   0.001  1
(DH663233) Rattus norvegicus DNA, BAC clone: RNB1-210H04, 3'...    56   0.001  1
(AC181725) Strongylocentrotus purpuratus clone R3-1039D03, W...    54   0.004  1
(AC176151) Strongylocentrotus purpuratus clone R3-2I13, WORK...    50   0.014  3
(AL513345) Mouse DNA sequence from clone RP23-129N7 on chrom...    52   0.014  1
(AC115847) Mus musculus chromosome 5, clone RP24-245J15, com...    52   0.014  1
(AC141680) Apis mellifera clone CH224-55I19, WORKING DRAFT S...    52   0.014  1
(AC141670) Apis mellifera clone CH224-54J8, *** SEQUENCING I...    52   0.014  1
(AC116053) Rattus norvegicus clone CH230-10J9, *** SEQUENCIN...    52   0.014  1
(AC095617) Rattus norvegicus clone CH230-8G3, *** SEQUENCING...    52   0.014  1
(CU896649) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    52   0.014  1
(CU855896) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    52   0.014  1
(AC181302) Strongylocentrotus purpuratus clone R3-115H16, WO...    52   0.014  1
(AC179604) Strongylocentrotus purpuratus clone R3-1029A14, W...    52   0.014  1
(BH304722) CH230-85G22.TJ CHORI-230 Segment 1 Rattus norvegi...    52   0.014  1
(DH515870) Rattus norvegicus DNA, BAC clone: RNB1-011I21, 3'...    52   0.014  1
(FE088438) LV_GL_RA36K17r Litopenaeus vannamei gills cDNA li...    52   0.014  1
(AC176022) Strongylocentrotus purpuratus clone R3-17P11, WOR...    50   0.015  2
(FF553045) MOPFI14TF MOP Vigna unguiculata cDNA 5', mRNA seq...    36   0.045  2
(BX927244) Zebrafish DNA sequence from clone CH211-116O3 in ...    50   0.057  1
(FM162578) Trypanosoma brucei Lister 427 surface glycoprotei...    50   0.057  1
(AC128521) Rattus norvegicus clone CH230-29N17, *** SEQUENCI...    50   0.057  1
(AC095794) Rattus norvegicus clone CH230-9F15, *** SEQUENCIN...    50   0.057  1
(CR940352) Theileria annulata genomic DNA chromosome 3.            50   0.057  1
(AL844509) Plasmodium falciparum chromosome 13.                    50   0.057  1
(AL049184) Plasmodium falciparum DNA *** SEQUENCING IN PROGR...    50   0.057  1
(AC181182) Strongylocentrotus purpuratus clone R3-14O14, WOR...    50   0.057  1
(AC180300) Strongylocentrotus purpuratus clone R3-3119M01, W...    50   0.057  1
(AC180279) Strongylocentrotus purpuratus clone R3-3119O19, W...    50   0.057  1
(AC180069) Strongylocentrotus purpuratus clone R3-28M7, WORK...    50   0.057  1
(AC179779) Strongylocentrotus purpuratus clone R3-1015J15, W...    50   0.057  1
(AC179103) Strongylocentrotus purpuratus clone R3-4011E1, WO...    50   0.057  1
(AC179093) Strongylocentrotus purpuratus clone R3-4011B12, W...    50   0.057  1
(AC178769) Strongylocentrotus purpuratus clone R3-19H10, WOR...    50   0.057  1
(AC176606) Strongylocentrotus purpuratus clone R3-3079F5, WO...    50   0.057  1
(AC176212) Strongylocentrotus purpuratus clone R3-3063L12, W...    50   0.057  1
(AC173980) Strongylocentrotus purpuratus clone R3-14E12, WOR...    50   0.057  1
(T09672) 0251m7 gmbPfHB3.1, G. Roman Reddy Plasmodium falcip...    50   0.057  1
(AA550389) 1537m3 gmbPfHB3.1, G. Roman Reddy Plasmodium falc...    50   0.057  1
(EC823834) SME00005162 esmbsro2 Sawyeria marylandensis cDNA,...    50   0.057  1
(CT009751) Trypanosoma brucei chromosome 9, unassembled cont...    44   0.12   2
(AC176583) Strongylocentrotus purpuratus clone R3-3077I12, W...    38   0.13   2
(AC091243) Trypanosoma brucei chromosome II clone RPCI93-29K...    34   0.13   2
(AZ207849) SP_0135_A2_F10_SP6E Strongylocentrotus purpuratus...    38   0.17   2
(AZ181543) SP_0184_B1_H03_SP6E Strongylocentrotus purpuratus...    38   0.18   2
(AZ167232) SP_0094_B2_F12_SP6E Strongylocentrotus purpuratus...    44   0.19   2
(BX664607) Zebrafish DNA sequence from clone CH211-132B12 in...    48   0.22   1
(BX548246) Zebrafish DNA sequence from clone CH211-274P15 in...    48   0.22   1
(AC165428) Strongylocentrotus purpuratus BAC clone contig co...    48   0.22   1
(AC116925) Dictyostelium discoideum chromosome 2 map 4189423...    48   0.22   1
(AC201050) Strongylocentrotus purpuratus clone R3-12N13, WOR...    48   0.22   1
(AC181298) Strongylocentrotus purpuratus clone R3-115H21, WO...    48   0.22   1
(AC181291) Strongylocentrotus purpuratus clone R3-4017D09, W...    48   0.22   1
(AC180594) Strongylocentrotus purpuratus clone R3-3092I18, W...    48   0.22   1
(AC180376) Strongylocentrotus purpuratus clone R3-3113A18, W...    48   0.22   1
(AC178185) Strongylocentrotus purpuratus clone R3-3082E2, WO...    48   0.22   1
(AC178061) Strongylocentrotus purpuratus clone R3-3056L18, W...    48   0.22   1
(AC177178) Strongylocentrotus purpuratus clone R3-1035A21, W...    48   0.22   1
(AC176547) Strongylocentrotus purpuratus clone R3-3076B14, W...    48   0.22   1
(AC174936) Strongylocentrotus purpuratus clone R3-4016H14, W...    48   0.22   1
(AC174739) Strongylocentrotus purpuratus clone R3-1008D12, W...    48   0.22   1
(AC173369) Strongylocentrotus purpuratus clone R3-3102B8, WO...    48   0.22   1
(AC168506) Strongylocentrotus purpuratus clone R3-3117B23, W...    48   0.22   1
(AZ156027) SP_0041_A1_F06_SP6E Strongylocentrotus purpuratus...    48   0.22   1
(FH064716) CHO_OF3597xj01f1.ab1 CHO_OF3 Nicotiana tabacum ge...    48   0.22   1
(EJ768534) 1092963347179 Global-Ocean-Sampling_GS-30-02-01-1...    48   0.22   1
(EI819388) POTEY58TF Solanum tuberosum RHPOTKEY BAC ends Sol...    48   0.22   1
(DH767451) Rattus norvegicus DNA, BAC clone: RNB1-351C11, 3'...    48   0.22   1
(BG737874) fo97f02.y1 zebrafish gridded kidney Danio rerio c...    48   0.22   1
(FE129169) LV_HP_RA11I06r Litopenaeus vannamei hepatopancrea...    48   0.22   1
(FE052271) LV_ES_RA17D19f Litopenaeus vannamei eyestalk cDNA...    48   0.22   1
(AC178500) Strongylocentrotus purpuratus clone R3-3032L5, WO...    38   0.27   5
(DY891449) CeleSEQ10145 Cunninghamella elegans pBluescript (...    38   0.33   2
(AC179054) Strongylocentrotus purpuratus clone R3-4005I14, W...    36   0.48   2
(AC116982) Dictyostelium discoideum chromosome 2 map 3622643...    36   0.55   5
(CI998827) Marsupenaeus japonicus cDNA, clone:YAQ02A01NGRM00...    36   0.70   2
(BX323887) Zebrafish DNA sequence from clone CH211-274C22 in...    46   0.88   1
(BX322567) Zebrafish DNA sequence from clone CH211-240G9 in ...    46   0.88   1
(AC158607) Mus musculus 10 BAC RP23-183G4 (Roswell Park Canc...    46   0.88   1
(AC156270) Mus musculus 10 BAC RP24-289H6 (Roswell Park Canc...    46   0.88   1
(AC153936) Mus musculus 10 BAC RP24-114G19 (Roswell Park Can...    46   0.88   1
(AC153935) Mus musculus 10 BAC RP24-273A2 (Roswell Park Canc...    46   0.88   1
(AC153509) Mus musculus 10 BAC RP23-60H16 (Roswell Park Canc...    46   0.88   1
(AC150314) Mus musculus BAC clone RP23-269O24 from chromosom...    46   0.88   1
(AC140787) Mus musculus BAC clone RP23-411H17 from 10, compl...    46   0.88   1
(AC193032) Pan troglodytes BAC clone CH251-656E15 from chrom...    46   0.88   1
(AM428326) Vitis vinifera contig VV78X019797.8, whole genome...    46   0.88   1
(DD367313) Useful microorganisms for industry.                     46   0.88   1
(AL929358) Plasmodium falciparum strain 3D7, chromosome 9; s...    46   0.88   1
(AF022984) Caenorhabditis elegans cosmid ZK488, complete seq...    46   0.88   1
(Y13187) Homo sapiens partial DMD gene, intron 11, isolate 381.    46   0.88   1
(Y13186) Homo sapiens partial DMD gene, mutated intron 11, i...    46   0.88   1
(AC078989) Homo sapiens Xp BAC RP11-769N24 (Roswell Park Can...    46   0.88   1
(AC004468) Homo sapiens Xp21 PAC RPCI1-37A12 containing exon...    46   0.88   1
(AC130092) Rattus norvegicus clone CH230-102M17, *** SEQUENC...    46   0.88   1

>(AC116979) Dictyostelium discoideum chromosome 2 map 6445720-6776760
              strain AX4, complete sequence.
          Length = 331039

 Score =  248 bits (125), Expect(2) = 3e-91
 Identities = 125/125 (100%)
 Strand = Plus / Minus


Query: 118    aaaatatggaagaaattcaaccatcatcatcaaaagaaacggaatctattaatagtaatg 177
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 291604 aaaatatggaagaaattcaaccatcatcatcaaaagaaacggaatctattaatagtaatg 291545


Query: 178    aaaatgataatgataataaaattagtactacaccagttatttctatatcaacatttataa 237
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 291544 aaaatgataatgataataaaattagtactacaccagttatttctatatcaacatttataa 291485


Query: 238    agagt 242
              |||||
Sbjct: 291484 agagt 291480

 Score =  119 bits (60), Expect(2) = 3e-91
 Identities = 60/60 (100%)
 Strand = Plus / Minus


Query: 250    gtgcatcaacaagtacatcaccaccgaaatctggttcattattatcaattcaaagaactt 309
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 291472 gtgcatcaacaagtacatcaccaccgaaatctggttcattattatcaattcaaagaactt 291413

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 251,496,376
Number of extensions: 17549697
Number of successful extensions: 1552975
Number of sequences better than 10.0: 526
Length of query: 378
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 355
Effective length of database: 93,106,754,628
Effective search space: 33052897892940
Effective search space used: 33052897892940
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06692-1 (Contig-U06692-1Q) /CSM_Contig/Contig-U06692-1Q.Seq.d
         (378 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: 245,898,328
Number of extensions: 2557196
Number of successful extensions: 3433
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3429
Number of HSP's successfully gapped: 0
Length of query: 126
Length of database: 1,040,966,779
Length adjustment: 91
Effective length of query: 35
Effective length of database: 749,376,844
Effective search space: 26228189540
Effective search space used: 26228189540
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: 0.98  gvh: 0.51  alm: 0.20  top: 0.50  tms: 0.13  mit: 0.26  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: 1.00  m3b: 0.00  m_ : 0.00 

	 40.0 %: endoplasmic reticulum
	 16.0 %: plasma membrane
	 12.0 %: mitochondrial
	  8.0 %: extracellular, including cell wall
	  4.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: Golgi
	  4.0 %: nuclear
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U06692-1 is end
VS (DIR, S) 2
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