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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U12879-1
Contig ID Contig-U12879-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12879-1 (Contig-U12879-1Q) /CSM_Contig/Contig-U12879-1Q.Seq.d
NNNNNNNNNNCCNCCTAAAACTTATTTANANCAACAAGGTNATGNAAATN
GATTTTCACCACCACCACCATNCTTTTTAACACCACATTNAGTATNACCA
ACTNCACCACCTCAAACAACACCACCATCAA
Gap no gap
Contig length 131
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U12879
List of clone(s) 

est1=CFI190Z,1,122
Translated Amino Acid sequence 
XXXPPKTYLXQQGXXNXFSPPPPXFLTPHXVXPTXPPQTTPPS
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxx*nlfxxtrxxkxifttttxlfnttxsxtnxttsnntti


Frame B:
XXXPPKTYLXQQGXXNXFSPPPPXFLTPHXVXPTXPPQTTPPS


Frame C:
xxxxlklixxnkvmxxdfhhhhhxf*hhixyxqlhhlkqhhhq
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12879-1 (Contig-U12879-1Q)
/CSM_Contig/Contig-U12879-1Q.Seq.d
         (131 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12879-1 (Contig-U12879-1Q) /CSM_Contig/Conti...   180  2e-46
Contig-U12160-1 (Contig-U12160-1Q) /CSM_Contig/Conti...    36  0.008
Contig-U11884-1 (Contig-U11884-1Q) /CSM_Contig/Conti...    34  0.033
Contig-U08981-1 (Contig-U08981-1Q) /CSM_Contig/Conti...    34  0.033
Contig-U14849-1 (Contig-U14849-1Q) /CSM_Contig/Conti...    32  0.13
Contig-U13130-1 (Contig-U13130-1Q) /CSM_Contig/Conti...    32  0.13
Contig-U12184-1 (Contig-U12184-1Q) /CSM_Contig/Conti...    32  0.13
Contig-U12071-1 (Contig-U12071-1Q) /CSM_Contig/Conti...    32  0.13
Contig-U11813-1 (Contig-U11813-1Q) /CSM_Contig/Conti...    32  0.13
Contig-U11737-1 (Contig-U11737-1Q) /CSM_Contig/Conti...    32  0.13

>Contig-U12879-1 (Contig-U12879-1Q) /CSM_Contig/Contig-U12879-1Q.Seq.d
          Length = 131

 Score =  180 bits (91), Expect = 2e-46
 Identities = 118/118 (100%)
 Strand = Plus / Plus

                                                                       
Query: 14  cctaaaacttatttanancaacaaggtnatgnaaatngattttcaccaccaccaccatnc 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 14  cctaaaacttatttanancaacaaggtnatgnaaatngattttcaccaccaccaccatnc 73

                                                                     
Query: 74  tttttaacaccacattnagtatnaccaactncaccacctcaaacaacaccaccatcaa 131
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 74  tttttaacaccacattnagtatnaccaactncaccacctcaaacaacaccaccatcaa 131


>Contig-U12160-1 (Contig-U12160-1Q) /CSM_Contig/Contig-U12160-1Q.Seq.d
          Length = 2311

 Score = 36.2 bits (18), Expect = 0.008
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 113 caaacaacaccaccatca 130
           ||||||||||||||||||
Sbjct: 140 caaacaacaccaccatca 157


>Contig-U11884-1 (Contig-U11884-1Q) /CSM_Contig/Contig-U11884-1Q.Seq.d
          Length = 835

 Score = 34.2 bits (17), Expect = 0.033
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 55  ttcaccaccaccaccat 71
           |||||||||||||||||
Sbjct: 400 ttcaccaccaccaccat 416


  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: 2451
Number of Sequences: 6905
Number of extensions: 2451
Number of successful extensions: 1192
Number of sequences better than 10.0: 402
length of query: 131
length of database: 5,674,871
effective HSP length: 14
effective length of query: 117
effective length of database: 5,578,201
effective search space: 652649517
effective search space used: 652649517
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. 4
Homology vs DNA 
Query= Contig-U12879-1 (Contig-U12879-1Q) /CSM_Contig/Contig-U12879-1Q.Seq.d
         (131 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

(BJ375191) Dictyostelium discoideum cDNA clone:ddc17c23, 3' ...   180   7e-42  1
(AC115584) Dictyostelium discoideum chromosome 2 map complem...   141   6e-30  1
(DT554539) EST1065179 GH_TMO Gossypium hirsutum cDNA, mRNA s...    38   0.032  2
(AC105495) Rattus norvegicus clone CH230-216J16, WORKING DRA...    36   0.041  2
(AC106421) Rattus norvegicus clone CH230-126J7, *** SEQUENCI...    36   0.042  2
(AC103040) Rattus norvegicus clone CH230-222O5, WORKING DRAF...    36   0.043  2
(DH643412) Rattus norvegicus DNA, BAC clone: RNB1-183N20, 5'...    36   0.055  2
(X59828) Human chromosome 22 flanking hypervariable simple r...    36   0.12   2
(DY637767) PU2_plate16_H24 PU2 Prunus persica cDNA similar t...    38   0.29   2
(DY652120) PU4_plate55_N15 PU4 Prunus persica cDNA similar t...    38   0.31   2
(EL484257) CHUM6103.b1_N14.ab1 CHU(LMS) puzzle sunflower Hel...    38   0.44   2
(AC124744) Mus musculus BAC clone RP23-223E16 from 13, compl...    36   0.58   2
(AC168631) Strongylocentrotus purpuratus clone R3-3018O21, W...    32   0.58   2
(AC180775) Strongylocentrotus purpuratus clone R3-3074H07, W...    32   0.59   2
(AC184620) Strongylocentrotus purpuratus clone R3-3074H8, WO...    32   0.59   2
(AC160444) Bos taurus clone CH240-83N22, WORKING DRAFT SEQUE...    36   0.59   2
(AC180548) Strongylocentrotus purpuratus clone R3-3097C15, W...    32   0.59   2
(AC125190) Mus musculus BAC clone RP23-288O24 from chromosom...    36   0.59   2
(AC133490) Rattus norvegicus clone rp32-162c1, complete sequ...    44   1.1    1
(AC123086) Rattus norvegicus clone CH230-10P9, WORKING DRAFT...    44   1.1    1
(AC111335) Rattus norvegicus clone CH230-239H8, *** SEQUENCI...    30   2.0    2
(AP001751) Homo sapiens genomic DNA, chromosome 21q, section...    32   2.0    2
(AC106673) Rattus norvegicus clone CH230-108J3, WORKING DRAF...    32   2.1    2
(AC126661) Rattus norvegicus clone CH230-227I22, *** SEQUENC...    30   2.1    2
(AC094741) Rattus norvegicus clone CH230-5C12, *** SEQUENCIN...    32   2.1    2
(AC112619) Rattus norvegicus clone CH230-233I2, *** SEQUENCI...    32   2.1    2
(AC095114) Rattus norvegicus clone CH230-7L7, WORKING DRAFT ...    32   2.1    2
(AC094160) Rattus norvegicus clone CH230-2M24, *** SEQUENCIN...    30   2.1    2
(AC129672) Rattus norvegicus clone CH230-331L13, WORKING DRA...    30   2.1    2
(AC097388) Rattus norvegicus clone CH230-8O5, WORKING DRAFT ...    32   2.1    2
(AC120330) Rattus norvegicus clone CH230-233E9, *** SEQUENCI...    30   2.1    2
(AC128200) Rattus norvegicus clone CH230-33A7, WORKING DRAFT...    30   2.1    2
(AC133049) Rattus norvegicus clone CH230-18I14, WORKING DRAF...    30   2.1    2
(AC097023) Rattus norvegicus BAC CH230-35L12 (Children's Hos...    30   2.1    2
(AC099442) Rattus norvegicus clone CH230-193A11, WORKING DRA...    30   2.1    2
(AC134134) Rattus norvegicus clone CH230-175I17, *** SEQUENC...    32   2.1    2
(AC134810) Rattus norvegicus clone CH230-249N3, WORKING DRAF...    30   2.1    2
(AC121346) Rattus norvegicus chromosome 1 clone RP32-276L6 m...    32   2.1    2
(AP001933) Homo sapiens genomic DNA, chromosome 18q23 clone:...    32   2.1    2
(AC121968) Mus musculus BAC clone RP24-272N4 from chromosome...    30   2.1    2
(AC140145) Homo sapiens chromosome 5 clone RP11-244N5, WORKI...    32   2.1    2
(AC169997) Macaca mulatta clone CH250-141E20, WORKING DRAFT ...    32   2.1    2
(AC126496) Rattus norvegicus clone CH230-444G1, WORKING DRAF...    32   2.1    2
(AC172243) Macaca mulatta clone CH250-384J16, WORKING DRAFT ...    32   2.1    2
(AC015599) Homo sapiens chromosome , clone RP11-45B19, compl...    30   2.1    2
(AP001046) Homo sapiens genomic DNA, chromosome 21, clone:KB...    32   2.1    2
(AC184511) Strongylocentrotus purpuratus clone R3-3121C2, WO...    32   2.2    2
(AC124788) Homo sapiens clone RP11-1293A7, 3 ordered pieces.       30   2.2    2
(AC176356) Strongylocentrotus purpuratus clone R3-3053H11, W...    32   2.2    2
(AC105225) Homo sapiens chromosome 8, clone RP11-775E18, com...    30   2.2    2
(AC008888) Homo sapiens chromosome 19 clone CTD-2221F12, com...    32   2.2    2
(AC183517) Oryctolagus cuniculus clone LB1-171O9, WORKING DR...    32   2.2    2
(AC177225) Strongylocentrotus purpuratus clone R3-40J19, WOR...    32   2.2    2
(EC691434) JLE00004240 Jakoba libera Company (STANDARD) Jako...    30   2.9    2
(DE222701) Trifolium pratense DNA, clone:RCG14221.                 30   2.9    2
(DE222596) Trifolium pratense DNA, clone:RCG14090.                 30   2.9    2
(DE220515) Trifolium pratense DNA, clone:RCG11613.                 30   2.9    2
(DE222653) Trifolium pratense DNA, clone:RCG14161.                 30   3.0    2
(DE222409) Trifolium pratense DNA, clone:RCG13875.                 30   3.0    2
(DE222337) Trifolium pratense DNA, clone:RCG13784.                 30   3.0    2
(DE217674) Trifolium pratense DNA, clone:RCG08193.                 30   3.0    2
(FG933185) UCRVU09_CCNT12355_b1 Cowpea UCR 707 Mixed Tissue ...    38   3.4    2
(FD878417) CBHO2044.fwd CBHO Volvox carteri f. nagariensis f...    42   4.2    1
(FD878416) CBHO2044.rev CBHO Volvox carteri f. nagariensis f...    42   4.2    1
(FD845983) CBHA12784.rev CBHA Volvox carteri f. nagariensis ...    42   4.2    1
(AP008211) Oryza sativa (japonica cultivar-group) genomic DN...    30   5.1    2
(AY630349) Strongylocentrotus franciscanus clone 53 microsat...    32   5.2    2
(BZ037899) oeh82a06.g1 B.oleracea002 Brassica oleracea genom...    34   5.3    2
(EF424219) Homo sapiens cell-line somatic cell hybrid F1H4 c...    32   5.4    2
(CO549137) LyEST663 Sea lamprey LyEST Petromyzon marinus cDN...    34   6.8    2
(AC110966) Rattus norvegicus clone CH230-123M20, WORKING DRA...    30   7.3    2
(AC135411) Rattus norvegicus clone CH230-2N13, *** SEQUENCIN...    30   7.4    2
(AP001759) Homo sapiens genomic DNA, chromosome 21q, section...    30   7.4    2
(AC094881) Rattus norvegicus clone CH230-5O7, WORKING DRAFT ...    30   7.5    2
(AC111701) Rattus norvegicus clone CH230-29D9, WORKING DRAFT...    30   7.5    2
(DE213731) Trifolium pratense DNA, clone:RCG02021.                 36   7.5    2
(AC116193) Rattus norvegicus clone CH230-236C24, *** SEQUENC...    30   7.5    2
(AC112062) Rattus norvegicus clone CH230-239E15, *** SEQUENC...    30   7.5    2
(AC095469) Rattus norvegicus clone CH230-7H17, *** SEQUENCIN...    30   7.5    2
(AC112860) Rattus norvegicus clone CH230-164D22, WORKING DRA...    30   7.5    2
(AC093987) Rattus norvegicus clone CH230-36D18, WORKING DRAF...    30   7.5    2
(AC114058) Rattus norvegicus clone CH230-196M2, *** SEQUENCI...    30   7.6    2
(AC131859) Rattus norvegicus clone CH230-198G14, WORKING DRA...    30   7.6    2
(AC119394) Rattus norvegicus clone CH230-11E24, WORKING DRAF...    30   7.6    2
(AC098108) Rattus norvegicus clone CH230-121A23, WORKING DRA...    30   7.6    2
(AC137290) Rattus norvegicus clone CH230-unknown, *** SEQUEN...    30   7.6    2
(AC097097) Rattus norvegicus clone CH230-189N20, WORKING DRA...    30   7.6    2
(AC122629) Rattus norvegicus clone CH230-102A4, WORKING DRAF...    30   7.6    2
(AC095098) Rattus norvegicus clone CH230-7I17, *** SEQUENCIN...    30   7.6    2
(AC125687) Rattus norvegicus clone CH230-39G12, WORKING DRAF...    30   7.6    2
(AC114157) Rattus norvegicus clone CH230-152H16, *** SEQUENC...    30   7.6    2
(AC106236) Rattus norvegicus clone CH230-131J10, WORKING DRA...    30   7.6    2
(AC141493) Rattus norvegicus clone CH230-179M7, WORKING DRAF...    30   7.6    2
(AC159813) Mus musculus BAC clone RP23-386L9 from chromosome...    30   7.6    2
(AC181297) Strongylocentrotus purpuratus clone R3-3040L15, W...    30   7.6    2
(AC135370) Rattus norvegicus clone CH230-457O20, *** SEQUENC...    30   7.7    2
(AC182991) Bos taurus clone CH240-172G1, WORKING DRAFT SEQUE...    30   7.7    2
(AC153367) Mus musculus 10 BAC RP23-182A11 (Roswell Park Can...    30   7.7    2
(AC019225) Homo sapiens chromosome 1 clone RP11-550G16, WORK...    30   7.7    2
(AP001876) Homo sapiens genomic DNA, chromosome 11 clone:CTD...    30   7.7    2

>(BJ375191) Dictyostelium discoideum cDNA clone:ddc17c23, 3' end,
           single read.
          Length = 122

 Score =  180 bits (91), Expect = 7e-42
 Identities = 118/118 (100%)
 Strand = Plus / Minus


Query: 14  cctaaaacttatttanancaacaaggtnatgnaaatngattttcaccaccaccaccatnc 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 119 cctaaaacttatttanancaacaaggtnatgnaaatngattttcaccaccaccaccatnc 60


Query: 74  tttttaacaccacattnagtatnaccaactncaccacctcaaacaacaccaccatcaa 131
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 59  tttttaacaccacattnagtatnaccaactncaccacctcaaacaacaccaccatcaa 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 83,175,920
Number of extensions: 7464934
Number of successful extensions: 2510690
Number of sequences better than 10.0: 133
Length of query: 131
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 109
Effective length of database: 93,199,600,587
Effective search space: 10158756463983
Effective search space used: 10158756463983
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7. 5
Homology vs Protein 
Query= Contig-U12879-1 (Contig-U12879-1Q) /CSM_Contig/Contig-U12879-1Q.Seq.d
         (131 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AM494940_72(AM494940|pid:none) Leishmania braziliensis chromosom...    33   3.1

>AM494940_72(AM494940|pid:none) Leishmania braziliensis chromosome 3.
          Length = 1295

 Score = 33.1 bits (74), Expect = 3.1
 Identities = 9/23 (39%), Positives = 11/23 (47%)
 Frame = -2

Query: 127  WWCCLRWXSWXYXMWC*KXWWWW 59
            WW    W  W +  W  + WWWW
Sbjct: 1274 WW----WWWWRWWWWWRRRWWWW 1292

 Score = 32.7 bits (73), Expect = 4.0
 Identities = 10/23 (43%), Positives = 12/23 (52%)
 Frame = -2

Query: 127  WWCCLRWXSWXYXMWC*KXWWWW 59
            WW   RW  W +  W  + WWWW
Sbjct: 1268 WW---RWRWWWWWWW--RWWWWW 1285

 Score = 32.7 bits (73), Expect = 4.0
 Identities = 10/23 (43%), Positives = 11/23 (47%)
 Frame = -2

Query: 127  WWCCLRWXSWXYXMWC*KXWWWW 59
            WW   RW  W    W  + WWWW
Sbjct: 1275 WWWWWRWWWW----WRRRWWWWW 1293

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: 62,201,830
Number of extensions: 380421
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 565
Number of HSP's successfully gapped: 3
Length of query: 43
Length of database: 1,051,180,864
Length adjustment: 17
Effective length of query: 26
Effective length of database: 996,159,361
Effective search space: 25900143386
Effective search space used: 25900143386
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: 0.83  gvh: 0.37  alm: 0.63  top: 0.53  tms: 0.00  mit: 0.43  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.00  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 %: mitochondrial
	 24.0 %: cytoplasmic
	 20.0 %: nuclear
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for Contig-U12879-1 is mit
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) 0
CF (FL, S) 1
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0