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Dicty_cDB
Contig List | Clone List | cDNA Library List
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U12821-1
Contig ID Contig-U12821-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12821-1 (Contig-U12821-1Q) /CSM_Contig/Contig-U12821-1Q.Seq.d
TTTTTTTTTTTTAAAAAAAAAACCTCAATAATCTTAAAATTTTAATATTA
ATAGAAATATCATTATTTTTTTTTTTAAAATTTATAATAGTAGATATAGA
AACCAACATAAAAAAATAAAAAATAAAAAAATAAAAAAAATAAAAATAAA
ACAATAATAAAAATTCCAAGTAAAATAAATAATTAAGAAAAAAAAAA
Gap no gap
Contig length 197
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 1963767
End point 1963571
Strand (PLUS/MINUS) MINUS
Number of clones 6
Number of EST 6
Link to clone list U12821
List of clone(s) 

est1=AHN173Z,-35,156
est2=CHG467F,27,192
est3=AHO604F,30,197
est4=AHO802Z,30,155
est5=AHP427Z,36,156
est6=CHR408F,81,192
Translated Amino Acid sequence 
ffflkkkpq*s*NFNINRNIIIFFFKIYNSRYRNQHKKIKNKKIKKIKIKQ**kfqvk*i
ikkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
ffffkkktsiilkf*y**kyhyfff*nl***i*kpt*knkk*knkknknktiikipskin
n*ekk


Frame B:
ffflkkkpq*s*NFNINRNIIIFFFKIYNSRYRNQHKKIKNKKIKKIKIKQ**kfqvk*i
ikkkk


Frame C:
fff*kknlnnlkililieislffflkfiivdietnikk*kikk*kk*k*nnnknsk*nk*
lrkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12821-1 (Contig-U12821-1Q)
/CSM_Contig/Contig-U12821-1Q.Seq.d
         (197 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12821-1 (Contig-U12821-1Q) /CSM_Contig/Conti...   105  2e-23
Contig-U12246-1 (Contig-U12246-1Q) /CSM_Contig/Conti...    40  8e-04
Contig-U14392-1 (Contig-U14392-1Q) /CSM_Contig/Conti...    34  0.052
Contig-U03801-1 (Contig-U03801-1Q) /CSM_Contig/Conti...    34  0.052
Contig-U03720-1 (Contig-U03720-1Q) /CSM_Contig/Conti...    34  0.052
Contig-U01854-1 (Contig-U01854-1Q) /CSM_Contig/Conti...    34  0.052
Contig-U13870-1 (Contig-U13870-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U12434-1 (Contig-U12434-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U10386-1 (Contig-U10386-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U09546-1 (Contig-U09546-1Q) /CSM_Contig/Conti...    32  0.20

>Contig-U12821-1 (Contig-U12821-1Q) /CSM_Contig/Contig-U12821-1Q.Seq.d
          Length = 197

 Score =  105 bits (53), Expect = 2e-23
 Identities = 75/86 (87%)
 Strand = Plus / Plus

                                                                       
Query: 23  cctcaataatcttaaaattttaatattaatagaaatatcattannnnnnnnnnnaaaatt 82
           |||||||||||||||||||||||||||||||||||||||||||           ||||||
Sbjct: 23  cctcaataatcttaaaattttaatattaatagaaatatcattatttttttttttaaaatt 82

                                     
Query: 83  tataatagtagatatagaaaccaaca 108
           ||||||||||||||||||||||||||
Sbjct: 83  tataatagtagatatagaaaccaaca 108


 Score = 28.2 bits (14), Expect = 3.2
 Identities = 20/22 (90%)
 Strand = Plus / Minus

                                
Query: 29 taatcttaaaattttaatatta 50
          |||| |||||||||||| ||||
Sbjct: 50 taatattaaaattttaagatta 29


>Contig-U12246-1 (Contig-U12246-1Q) /CSM_Contig/Contig-U12246-1Q.Seq.d
          Length = 1186

 Score = 40.1 bits (20), Expect = 8e-04
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                                
Query: 34   ttaaaattttaatattaata 53
            ||||||||||||||||||||
Sbjct: 1120 ttaaaattttaatattaata 1101


 Score = 30.2 bits (15), Expect = 0.81
 Identities = 21/23 (91%)
 Strand = Plus / Plus

                                   
Query: 29   taatcttaaaattttaatattaa 51
            |||| ||||||||||||| ||||
Sbjct: 1104 taatattaaaattttaatcttaa 1126


>Contig-U14392-1 (Contig-U14392-1Q) /CSM_Contig/Contig-U14392-1Q.Seq.d
          Length = 798

 Score = 34.2 bits (17), Expect = 0.052
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 44  aatattaatagaaatat 60
           |||||||||||||||||
Sbjct: 609 aatattaatagaaatat 625


  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: 2585
Number of Sequences: 6905
Number of extensions: 2585
Number of successful extensions: 909
Number of sequences better than 10.0: 110
length of query: 197
length of database: 5,674,871
effective HSP length: 15
effective length of query: 182
effective length of database: 5,571,296
effective search space: 1013975872
effective search space used: 1013975872
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 2008.12. 4
Homology vs DNA 
Query= Contig-U12821-1 (Contig-U12821-1Q) /CSM_Contig/Contig-U12821-1Q.Seq.d
         (197 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

(AJ005398) Dictyostelium discoideum regA gene.                     86   6e-27  2
(U60170) Dictyostelium discoideum RegA (regA) gene, complete...    78   1e-24  2
(BJ365226) Dictyostelium discoideum cDNA clone:ddc34f18, 5' ...    78   1e-24  2
(BJ355631) Dictyostelium discoideum cDNA clone:dda57a19, 3' ...    72   8e-23  2
(BJ338096) Dictyostelium discoideum cDNA clone:dda60g02, 5' ...    72   8e-23  2
(BJ356344) Dictyostelium discoideum cDNA clone:dda60d02, 3' ...    72   8e-23  2
(BJ370986) Dictyostelium discoideum cDNA clone:ddc56p02, 5' ...    52   0.007  1
(BV065559) S212P6088FH6.T0 CZECHII/Ei Mus musculus STS genom...    50   0.028  1
(AC147152) Mus musculus BAC clone RP24-257J19 from 3, comple...    50   0.028  1
(AC124529) Mus musculus BAC clone RP23-411I8 from chromosome...    50   0.028  1
(AM449094) Vitis vinifera contig VV78X107954.3, whole genome...    50   0.028  1
(CU633315) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    48   0.11   1
(DX188994) OR_ABa0053P17.f OR_ABa Oryza ridleyi genomic clon...    32   0.25   3
(AC226018) Solanum lycopersicum chromosome 6 clone C06SLm007...    46   0.43   1
(AC216653) Solanum lycopersicum chromosome 6 clone C06HBa022...    46   0.43   1
(CT400877) Sus scrofa genomic clone CH242-406N19, genomic su...    46   0.43   1
(DB777112) Apis mellifera head cDNA, RIKEN full-length enric...    46   0.43   1
(DB771035) Apis mellifera head cDNA, RIKEN full-length enric...    46   0.43   1
(DB765673) Apis mellifera head cDNA, RIKEN full-length enric...    46   0.43   1
(DB762216) Apis mellifera head cDNA, RIKEN full-length enric...    46   0.43   1
(DB759099) Apis mellifera head cDNA, RIKEN full-length enric...    46   0.43   1
(AC197339) Zea mays chromosome 8 clone CH201-414A1; ZMMBBc04...    42   0.79   2
(AC130253) Rattus norvegicus clone CH230-50A6, WORKING DRAFT...    36   0.89   2
(AC108329) Rattus norvegicus clone CH230-303I19, WORKING DRA...    36   0.90   2
(AC136582) Rattus norvegicus clone CH230-8N14, WORKING DRAFT...    36   0.90   2
(AM435460) Vitis vinifera contig VV78X132558.5, whole genome...    42   1.3    3
(AC160443) Bos taurus clone CH240-83O21, WORKING DRAFT SEQUE...    44   1.7    1
(AC153190) Bos taurus clone CH240-29L9, WORKING DRAFT SEQUEN...    44   1.7    1
(AC117028) Rattus norvegicus clone CH230-263A13, WORKING DRA...    44   1.7    1
(CU468694) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   1.7    1
(AC173025) Bos taurus clone CH240-252H22, WORKING DRAFT SEQU...    44   1.7    1
(AC170251) Bos taurus clone CH240-202H17, WORKING DRAFT SEQU...    44   1.7    1
(ED829012) KI_R1004 Pro1 addition line Beta vulgaris subsp. ...    44   1.7    1
(AW334855) S40A9 AGS-1 Pneumocystis carinii cDNA 3', mRNA se...    44   1.7    1
(BA000021) Wigglesworthia glossinidia endosymbiont of Glossi...    44   1.7    1
(CD979572) QAG4e12.xg QAG Zea mays cDNA clone QAG4e12, mRNA ...    38   4.0    2
(AC152506) Pan troglodytes BAC clone RP43-4B9 from chromosom...    42   6.8    1
(AC146106) Pan troglodytes BAC clone RP43-5I17 from chromoso...    42   6.8    1
(AM477181) Vitis vinifera contig VV78X019152.8, whole genome...    42   6.8    1
(AM446414) Vitis vinifera contig VV78X165164.22, whole genom...    42   6.8    1
(DI072489) MODIFYING THE EXPRESSION OF THE FSH BETA GENE BY ...    42   6.8    1
(DI014066) MODIFYING THE EXPRESSION OF THE FSH BETA GENE BY ...    42   6.8    1
(DD010736) Diagnosis of known genetic Parameters within the ...    42   6.8    1
(BD393479) METHODS OF IMPROVING HOMOLOGOUS RECOMBINATION.          42   6.8    1
(BD393478) METHODS OF IMPROVING HOMOLOGOUS RECOMBINATION.          42   6.8    1
(BD211481) Modifying the expression of the FSH-beta gene by ...    42   6.8    1
(BD211479) Modifying the expression of the FSH-beta gene by ...    42   6.8    1
(AX344569) Sequence 20 from Patent WO0200932.                      42   6.8    1
(AX250675) Sequence 2 from Patent WO0168882.                       42   6.8    1
(AX250674) Sequence 1 from Patent WO0168882.                       42   6.8    1
(AR339722) Sequence 2 from patent US 6569681.                      42   6.8    1
(AR339721) Sequence 1 from patent US 6569681.                      42   6.8    1
(AR138911) Sequence 4 from patent US 6200778.                      42   6.8    1
(AR138909) Sequence 1 from patent US 6200778.                      42   6.8    1
(AC099509) Homo sapiens chromosome 5 clone RP11-254I22, comp...    42   6.8    1
(AC006004) Homo sapiens PAC clone RP4-803F10 from 7, complet...    42   6.8    1
(AC151378) Callithrix jacchus clone CH259-289F2, WORKING DRA...    42   6.8    1
(AC148165) Zea mays clone ZMMBBc0414A01, *** SEQUENCING IN P...    42   6.8    1
(AC127039) Rattus norvegicus clone CH230-82M19, WORKING DRAF...    42   6.8    1
(AC116190) Rattus norvegicus clone CH230-172H2, WORKING DRAF...    42   6.8    1
(AC112291) Rattus norvegicus clone CH230-183D19, *** SEQUENC...    42   6.8    1
(AC107131) Rattus norvegicus clone CH230-38C17, *** SEQUENCI...    42   6.8    1
(AC099213) Rattus norvegicus clone CH230-51F4, *** SEQUENCIN...    42   6.8    1
(CU582839) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   6.8    1
(CU582804) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   6.8    1
(CR940353) Theileria annulata genomic DNA chromosome 4.            42   6.8    1
(AC220524) Bos taurus clone CH240-355H9, WORKING DRAFT SEQUE...    42   6.8    1
(AC190648) Gossypium hirsutum chromosome UNKNOWN clone ZMMBB...    42   6.8    1
(AC187153) Zea mays chromosome 8 clone CH201-226K24; ZMMBBc0...    42   6.8    1
(AC185316) Zea mays chromosome 5 clone CH201-298O17; ZMMBBc0...    42   6.8    1
(AC171611) Bos taurus clone CH240-270O4, WORKING DRAFT SEQUE...    42   6.8    1
(ET965235) CHO_OF628xe07r1.ab1 CHO_OF Nicotiana tabacum geno...    42   6.8    1
(ET965170) CHO_OF628xe07f1.ab1 CHO_OF Nicotiana tabacum geno...    42   6.8    1
(ET787636) CHO_OF639xg15r1.ab1 CHO_OF Nicotiana tabacum geno...    42   6.8    1
(EK210403) 1095460097175 Global-Ocean-Sampling_GS-31-01-01-1...    42   6.8    1
(EK039582) 1092959502897 Global-Ocean-Sampling_GS-31-01-01-1...    42   6.8    1
(EK018318) 1092955254877 Global-Ocean-Sampling_GS-31-01-01-1...    42   6.8    1
(EJ547757) 1092959414511 Global-Ocean-Sampling_GS-29-01-01-1...    42   6.8    1
(EJ537533) 1092955270280 Global-Ocean-Sampling_GS-29-01-01-1...    42   6.8    1
(EJ308091) 1095390120341 Global-Ocean-Sampling_GS-27-01-01-1...    42   6.8    1
(EJ164177) 1092344059269 Global-Ocean-Sampling_GS-27-01-01-1...    42   6.8    1
(EJ085448) 1095460097394 Global-Ocean-Sampling_GS-26-01-01-1...    42   6.8    1
(DX446098) BE2009_M10_F IASMA L2 HindIII BAC library Vitis v...    42   6.8    1
(CU813393) A BAC library has been constructed from PN40024 g...    42   6.8    1
(CR866115) Sus scrofa BES.                                         42   6.8    1
(BH682504) BOHTJ39TR BO_2_3_KB Brassica oleracea genomic clo...    42   6.8    1
(DT954319) CFW132-E09.x1d-t SHGC-CFW Gasterosteus aculeatus ...    42   6.8    1
(BJ356744) Dictyostelium discoideum cDNA clone:dda61f08, 3' ...    42   6.8    1
(AX652505) Sequence 2375 from Patent WO03000898.                   36   9.0    2
(AX508884) Sequence 3579 from Patent WO0216655.                    36   9.0    2
(AL844509) Plasmodium falciparum chromosome 13.                    32   9.7    2

>(AJ005398) Dictyostelium discoideum regA gene.
          Length = 4617

 Score = 85.7 bits (43), Expect(2) = 6e-27
 Identities = 43/43 (100%)
 Strand = Plus / Plus


Query: 23   cctcaataatcttaaaattttaatattaatagaaatatcatta 65
            |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1565 cctcaataatcttaaaattttaatattaatagaaatatcatta 1607

 Score = 65.9 bits (33), Expect(2) = 6e-27
 Identities = 33/33 (100%)
 Strand = Plus / Plus


Query: 77   aaaatttataatagtagatatagaaaccaacat 109
            |||||||||||||||||||||||||||||||||
Sbjct: 1619 aaaatttataatagtagatatagaaaccaacat 1651

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 110,026,012
Number of extensions: 8889649
Number of successful extensions: 2648178
Number of sequences better than 10.0: 91
Length of query: 197
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 174
Effective length of database: 93,106,754,628
Effective search space: 16200575305272
Effective search space used: 16200575305272
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 4
Homology vs Protein 
Query= Contig-U12821-1 (Contig-U12821-1Q) /CSM_Contig/Contig-U12821-1Q.Seq.d
         (197 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: 78,445,277
Number of extensions: 407465
Number of successful extensions: 610
Number of sequences better than 10.0: 0
Number of HSP's gapped: 610
Number of HSP's successfully gapped: 0
Length of query: 65
Length of database: 1,051,180,864
Length adjustment: 37
Effective length of query: 28
Effective length of database: 931,428,181
Effective search space: 26079989068
Effective search space used: 26079989068
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: 26 (14.6 bits)
PSORT 

 psg: 0.83  gvh: 0.24  alm: 0.52  top: 0.53  tms: 0.00  mit: 0.52  mip: 0.00
 nuc: 0.24  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: 0.00  m3b: 0.00  m_ : 1.00 

	 36.0 %: nuclear
	 28.0 %: mitochondrial
	 28.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U12821-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 4
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 2
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0