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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-U14456-1
Contig ID Contig-U14456-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14456-1 (Contig-U14456-1Q) /CSM_Contig/Contig-U14456-1Q.Seq.d
TGTTGGCCTACTGGCAACAACAATCATATAATAATAATAATTCAACACAA
TCAATGTTATCATCATTTCCAACATTAAAAATAGTAAAAATAAATAATAA
ATTAAAAATTATTATAAAGTAAAAAAAAAANNNNNNNNN
Gap no gap
Contig length 139
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 1065749
End point 1065669
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U14456
List of clone(s) 

est1=CHP809F,1,130
Translated Amino Acid sequence 
LAYWQQQSYNNNNSTQSMLSSFPTLKIVKINNKLKIIIK*kkxxx
Translated Amino Acid sequence (All Frames) 
Frame A:
cwptgnnnhiiiiiqhnqcyhhfqh*k**k*iin*kll*skkkxxx


Frame B:
vgllattii****fntinviiisniknsknk**iknyykvkkkxxx


Frame C:
LAYWQQQSYNNNNSTQSMLSSFPTLKIVKINNKLKIIIK*kkxxx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14456-1 (Contig-U14456-1Q)
/CSM_Contig/Contig-U14456-1Q.Seq.d
         (139 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14456-1 (Contig-U14456-1Q) /CSM_Contig/Conti...   149  9e-37
Contig-U12054-1 (Contig-U12054-1Q) /CSM_Contig/Conti...    46  9e-06
Contig-U11594-1 (Contig-U11594-1Q) /CSM_Contig/Conti...    46  9e-06
Contig-U14315-1 (Contig-U14315-1Q) /CSM_Contig/Conti...    40  6e-04
Contig-U11802-1 (Contig-U11802-1Q) /CSM_Contig/Conti...    40  6e-04
Contig-U11698-1 (Contig-U11698-1Q) /CSM_Contig/Conti...    40  6e-04
Contig-U11500-1 (Contig-U11500-1Q) /CSM_Contig/Conti...    40  6e-04
Contig-U03583-1 (Contig-U03583-1Q) /CSM_Contig/Conti...    40  6e-04
Contig-U03281-1 (Contig-U03281-1Q) /CSM_Contig/Conti...    40  6e-04
Contig-U12446-1 (Contig-U12446-1Q) /CSM_Contig/Conti...    38  0.002

>Contig-U14456-1 (Contig-U14456-1Q) /CSM_Contig/Contig-U14456-1Q.Seq.d
          Length = 139

 Score =  149 bits (75), Expect = 9e-37
 Identities = 75/75 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  tgttggcctactggcaacaacaatcatataataataataattcaacacaatcaatgttat 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  tgttggcctactggcaacaacaatcatataataataataattcaacacaatcaatgttat 60

                         
Query: 61 catcatttccaacat 75
          |||||||||||||||
Sbjct: 61 catcatttccaacat 75


>Contig-U12054-1 (Contig-U12054-1Q) /CSM_Contig/Contig-U12054-1Q.Seq.d
          Length = 3002

 Score = 46.1 bits (23), Expect = 9e-06
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                   
Query: 1    tgttggcctactggcaacaacaa 23
            |||||||||||||||||||||||
Sbjct: 1577 tgttggcctactggcaacaacaa 1599


 Score = 34.2 bits (17), Expect = 0.035
 Identities = 23/25 (92%)
 Strand = Plus / Plus

                                     
Query: 17   acaacaatcatataataataataat 41
            |||||||||  ||||||||||||||
Sbjct: 1608 acaacaatctaataataataataat 1632


 Score = 28.2 bits (14), Expect = 2.2
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                          
Query: 28   ataataataataat 41
            ||||||||||||||
Sbjct: 1625 ataataataataat 1638


 Score = 28.2 bits (14), Expect = 2.2
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                          
Query: 28   ataataataataat 41
            ||||||||||||||
Sbjct: 1169 ataataataataat 1182


 Score = 28.2 bits (14), Expect = 2.2
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                          
Query: 28   ataataataataat 41
            ||||||||||||||
Sbjct: 1622 ataataataataat 1635


 Score = 26.3 bits (13), Expect = 8.6
 Identities = 13/13 (100%)
 Strand = Plus / Plus

                         
Query: 29   taataataataat 41
            |||||||||||||
Sbjct: 1053 taataataataat 1065


>Contig-U11594-1 (Contig-U11594-1Q) /CSM_Contig/Contig-U11594-1Q.Seq.d
          Length = 1508

 Score = 46.1 bits (23), Expect = 9e-06
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                 
Query: 1  tgttggcctactggcaacaacaa 23
          |||||||||||||||||||||||
Sbjct: 2  tgttggcctactggcaacaacaa 24


  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: 16,138
Number of Sequences: 6905
Number of extensions: 16138
Number of successful extensions: 12368
Number of sequences better than 10.0: 2340
length of query: 139
length of database: 5,674,871
effective HSP length: 15
effective length of query: 124
effective length of database: 5,571,296
effective search space: 690840704
effective search space used: 690840704
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2008.12.23
Homology vs DNA 
Query= Contig-U14456-1 (Contig-U14456-1Q) /CSM_Contig/Contig-U14456-1Q.Seq.d
         (139 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

(BJ370126) Dictyostelium discoideum cDNA clone:ddc53b04, 5' ...   145   4e-31  1
(BJ336904) Dictyostelium discoideum cDNA clone:dda55g14, 5' ...    46   5e-06  2
(BJ396922) Dictyostelium discoideum cDNA clone:dds44o09, 5' ...    46   3e-04  2
(BX511086) Zebrafish DNA sequence from clone DKEY-38P8 in li...    52   0.005  1
(BJ370112) Dictyostelium discoideum cDNA clone:ddc52n05, 5' ...    40   0.007  2
(BJ392204) Dictyostelium discoideum cDNA clone:dds26d20, 5' ...    40   0.007  2
(BJ370390) Dictyostelium discoideum cDNA clone:ddc53o22, 5' ...    36   0.007  3
(BJ397002) Dictyostelium discoideum cDNA clone:dds44p17, 5' ...    40   0.007  2
(BJ393963) Dictyostelium discoideum cDNA clone:dds33e12, 5' ...    40   0.007  2
(BJ327711) Dictyostelium discoideum cDNA clone:dda21p10, 5' ...    40   0.016  2
(AL360085) Human DNA sequence from clone RP11-505K1 on chrom...    50   0.019  1
(AC022797) Homo sapiens chromosome 6 clone RP11-281G13 map 6...    50   0.019  1
(EY307572) CAWX20550.rev CAWX Helobdella robusta Primary Ear...    46   0.032  2
(AC116956) Dictyostelium discoideum chromosome 2 map 1418423...    46   0.037  2
(AC105925) Homo sapiens BAC clone RP11-753I4 from 4, complet...    48   0.074  1
(AC178998) Strongylocentrotus purpuratus clone R3-3122N22, W...    48   0.074  1
(AC168317) Strongylocentrotus purpuratus clone R3-64O13, WOR...    48   0.074  1
(DW284443) UI-S-HH0-adz-k-09-0-UI.s1 UI-S-HH0 Euprymna scolo...    48   0.074  1
(DT310798) JGI_CAAX1994.fwd CAAX Pimephales promelas testis ...    48   0.074  1
(BJ392260) Dictyostelium discoideum cDNA clone:dds27b02, 5' ...    40   0.096  2
(AC209532) Medicago truncatula chromosome 7 BAC clone mth2-6...    36   0.17   2
(BJ325632) Dictyostelium discoideum cDNA clone:dda1o15, 5' e...    32   0.23   2
(CR376754) Zebrafish DNA sequence from clone CH211-254O14 in...    46   0.29   1
(G31344) UNH-006 Tilapia (fish) Oreochromis niloticus STS ge...    46   0.29   1
(AC211310) Populus trichocarpa clone POP017-I09, complete se...    46   0.29   1
(AC187022) Canis Familiaris chromosome 14, clone XX-314I11, ...    46   0.29   1
(AC184816) Canis familiaris chromosome 14, clone XX-46G21, c...    46   0.29   1
(AC137910) Canis familiaris clone RP81-221F11, WORKING DRAFT...    46   0.29   1
(AC201525) Strongylocentrotus purpuratus clone R3-3090B10, W...    46   0.29   1
(AC179098) Strongylocentrotus purpuratus clone R3-4011B7, WO...    46   0.29   1
(AC178533) Strongylocentrotus purpuratus clone R3-3031A4, WO...    46   0.29   1
(ET079371) QM0AAB8AD10RM1 CCER1 Citrus clementina genomic cl...    46   0.29   1
(EJ499607) 1095403608499 Global-Ocean-Sampling_GS-28-01-01-1...    46   0.29   1
(CW569392) OA_ABa0095H01.r OA_ABa Oryza australiensis genomi...    46   0.29   1
(DY894493) CeleSEQ14075 Cunninghamella elegans pBluescript (...    46   0.29   1
(DY893256) CeleSEQ12543 Cunninghamella elegans pBluescript (...    46   0.29   1
(BJ424639) Dictyostelium discoideum cDNA clone:ddv53h02, 5' ...    46   0.29   1
(BJ422137) Dictyostelium discoideum cDNA clone:ddv45a04, 5' ...    46   0.29   1
(BJ392405) Dictyostelium discoideum cDNA clone:dds27d15, 5' ...    46   0.29   1
(BJ370377) Dictyostelium discoideum cDNA clone:ddc53l20, 5' ...    46   0.29   1
(BX927225) Zebrafish DNA sequence from clone CH211-106F9 in ...    42   0.32   2
(BJ423103) Dictyostelium discoideum cDNA clone:ddv48g02, 5' ...    38   0.36   2
(BJ388738) Dictyostelium discoideum cDNA clone:dds16e06, 5' ...    38   0.38   2
(AL034557) Plasmodium falciparum MAL4P1.                           38   0.64   2
(AY360394) Oryza sativa (japonica cultivar-group) chromosome...    34   0.68   3
(AP004458) Oryza sativa Japonica Group genomic DNA, chromoso...    34   0.70   3
(BJ389201) Dictyostelium discoideum cDNA clone:dds17l21, 5' ...    34   0.76   2
(BJ411721) Dictyostelium discoideum cDNA clone:ddv5d16, 5' e...    36   0.80   2
(FG685579) G1143P329FM4.T0 Anolis carolinensis pooled normal...    36   0.81   2
(FG685627) G1143P329RM4.T0 Anolis carolinensis pooled normal...    36   0.82   2
(BJ336964) Dictyostelium discoideum cDNA clone:dda55e20, 5' ...    34   0.82   2
(BJ336787) Dictyostelium discoideum cDNA clone:dda55k03, 5' ...    36   0.85   2
(AC176751) Strongylocentrotus purpuratus clone R3-3097J4, WO...    42   0.88   2
(BJ336746) Dictyostelium discoideum cDNA clone:dda55b06, 5' ...    36   0.89   2
(BJ411720) Dictyostelium discoideum cDNA clone:ddv5d15, 5' e...    36   0.97   2
(BJ336828) Dictyostelium discoideum cDNA clone:dda55d09, 5' ...    36   1.1    2
(BJ415544) Dictyostelium discoideum cDNA clone:ddv22m21, 5' ...    34   1.1    2
(BJ393897) Dictyostelium discoideum cDNA clone:dds33e01, 5' ...    36   1.1    2
(AC114263) Dictyostelium discoideum chromosome 2 map 215673-...    42   1.1    2
(CU694274) Zebrafish DNA sequence from clone ZFOS-1762D12 in...    44   1.2    1
(CT033831) Zebrafish DNA sequence from clone CH211-215K2 in ...    44   1.2    1
(CR354390) Zebrafish DNA sequence from clone CH211-90K4 in l...    44   1.2    1
(CR318587) Zebrafish DNA sequence from clone CH211-171B20 in...    44   1.2    1
(BX927328) Zebrafish DNA sequence from clone CH211-10M4 in l...    44   1.2    1
(BX510305) Zebrafish DNA sequence from clone CH211-107P11 in...    44   1.2    1
(BX005418) Zebrafish DNA sequence from clone CH211-284C3.          44   1.2    1
(AC215853) Solanum lycopersicum chromosome 2 clone C02HBa003...    44   1.2    1
(AC215465) Solanum lycopersicum chromosome 2 clone C02SLe012...    44   1.2    1
(AC215353) Solanum lycopersicum chromosome 2 clone C02HBa001...    44   1.2    1
(AE014134) Drosophila melanogaster chromosome 2L, complete s...    44   1.2    1
(AC013424) Drosophila melanogaster clone BACR20C06, complete...    44   1.2    1
(AC136852) Rattus norvegicus clone CH230-77P6, *** SEQUENCIN...    44   1.2    1
(AC122591) Rattus norvegicus clone CH230-155K3, *** SEQUENCI...    44   1.2    1
(CU855777) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   1.2    1
(CU695005) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   1.2    1
(CU607104) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   1.2    1
(CU459163) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    44   1.2    1
(AC008333) Drosophila melanogaster strain y chromosome 2 clo...    44   1.2    1
(FH714264) CHO_OF5044xl15f1.ab1 CHO_OF5 Nicotiana tabacum ge...    44   1.2    1
(FH522231) CHO_OF4350xi09r1.ab1 CHO_OF4 Nicotiana tabacum ge...    44   1.2    1
(EK029337) 1092955397327 Global-Ocean-Sampling_GS-31-01-01-1...    44   1.2    1
(DH786488) Rattus norvegicus DNA, BAC clone: RNB1-376M08, 5'...    44   1.2    1
(DH649275) Rattus norvegicus DNA, BAC clone: RNB1-191K22, 5'...    44   1.2    1
(CW856428) sh2b8-36.g_063.ab1 Whole-genome shotgun library o...    44   1.2    1
(CW852475) OG_BBa0083E06.f OG_BBa Oryza glaberrima genomic c...    44   1.2    1
(DR437942) ACAC-aaa87d04.g1 Hydra EST UCI 7 Hydra magnipapil...    44   1.2    1
(DN566555) 92878581 Sea Urchin primary mesenchyme cell cDNA ...    44   1.2    1
(CN640581) 273D11_555702 Douglas-fir cDNA library PmIFG_73-6...    44   1.2    1
(CN639426) 242D04_553294 Douglas-fir cDNA library PmIFG_73-6...    44   1.2    1
(CN638564) 210E11_551462 Douglas-fir cDNA library PmIFG_73-6...    44   1.2    1
(CN637932) 158G05_550168 Douglas-fir cDNA library PmIFG_73-6...    44   1.2    1
(CN637449) 150C10_549199 Douglas-fir cDNA library PmIFG_73-6...    44   1.2    1
(CN636930) 141C01_548148 Douglas-fir cDNA library PmIFG_73-6...    44   1.2    1
(CN635706) 120F10_545677 Douglas-fir cDNA library PmIFG_73-6...    44   1.2    1
(CI031624) Oryza sativa Japonica Group cDNA, clone: 009-M089...    44   1.2    1
(FC851495) CBHN6868.fwd CBHN Metridium senile tentacle Metri...    44   1.2    1
(BJ370259) Dictyostelium discoideum cDNA clone:ddc53a18, 5' ...    36   1.2    2
(BJ363013) Dictyostelium discoideum cDNA clone:ddc24f18, 5' ...    36   1.2    2
(CU694672) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   1.2    2
(BJ392114) Dictyostelium discoideum cDNA clone:dds26n11, 5' ...    36   1.3    2

>(BJ370126) Dictyostelium discoideum cDNA clone:ddc53b04, 5' end,
          single read.
          Length = 130

 Score =  145 bits (73), Expect = 4e-31
 Identities = 73/73 (100%)
 Strand = Plus / Plus


Query: 1  tgttggcctactggcaacaacaatcatataataataataattcaacacaatcaatgttat 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  tgttggcctactggcaacaacaatcatataataataataattcaacacaatcaatgttat 60


Query: 61 catcatttccaac 73
          |||||||||||||
Sbjct: 61 catcatttccaac 73

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 104,315,339
Number of extensions: 11944542
Number of successful extensions: 6359549
Number of sequences better than 10.0: 279
Length of query: 139
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 117
Effective length of database: 93,199,600,587
Effective search space: 10904353268679
Effective search space used: 10904353268679
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7.11
Homology vs Protein 
Query= Contig-U14456-1 (Contig-U14456-1Q) /CSM_Contig/Contig-U14456-1Q.Seq.d
         (139 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 84,244,981
Number of extensions: 376412
Number of successful extensions: 1581
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1581
Number of HSP's successfully gapped: 0
Length of query: 46
Length of database: 1,051,180,864
Length adjustment: 20
Effective length of query: 26
Effective length of database: 986,449,684
Effective search space: 25647691784
Effective search space used: 25647691784
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: 25 (14.2 bits)
PSORT 

 psg: 0.91  gvh: 0.27  alm: 0.49  top: 0.80  tms: 0.00  mit: 0.42  mip: 0.00
 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 

	 44.0 %: nuclear
	 40.0 %: mitochondrial
	 16.0 %: cytoplasmic

>> prediction for Contig-U14456-1 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