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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-U04669-1
Contig ID Contig-U04669-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04669-1 (Contig-U04669-1Q) /CSM_Contig/Contig-U04669-1Q.Seq.d
ATAATTTCATATTTTTAATTATATCACATCATTAATTATTCACCAACACT
TTTTTTAAAATATTATCAATAAAATTTATGATATTAATATTTTTTTTTTA
TTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTATACTTTTATATT
TTTATAAATTAAGATACTTAAAAAATAAATCTTAAAAAAAAAAAAAAAAA
AAAAAAAA
Gap no gap
Contig length 208
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 2280437
End point 2280645
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U04669
List of clone(s) 

est1=SSC251F,1,209
Translated Amino Acid sequence 
*fhifnyitsliihqhff*NIINKIYDINIFFLLKKKKKKKKKKKYTFIFL*ikilkk*i
lkkkkkkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
iisyf*lyhiinysptlflkyyq*nl*y*yfffikkkkkkkkkkkvyfyifin*dt*kin
lkkkkkkkk


Frame B:
*fhifnyitsliihqhff*NIINKIYDINIFFLLKKKKKKKKKKKYTFIFL*ikilkk*i
lkkkkkkkk


Frame C:
nfifliishh*lftntffkilsikfmilifffy*kkkkkkkkkksillyfyklrylknks
*kkkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04669-1 (Contig-U04669-1Q)
/CSM_Contig/Contig-U04669-1Q.Seq.d
         (208 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04669-1 (Contig-U04669-1Q) /CSM_Contig/Conti...   161  4e-40
Contig-U14535-1 (Contig-U14535-1Q) /CSM_Contig/Conti...    38  0.004
Contig-U11335-1 (Contig-U11335-1Q) /CSM_Contig/Conti...    38  0.004
Contig-U12475-1 (Contig-U12475-1Q) /CSM_Contig/Conti...    36  0.014
Contig-U11699-1 (Contig-U11699-1Q) /CSM_Contig/Conti...    36  0.014
Contig-U11265-1 (Contig-U11265-1Q) /CSM_Contig/Conti...    36  0.014
Contig-U10619-1 (Contig-U10619-1Q) /CSM_Contig/Conti...    36  0.014
Contig-U05079-1 (Contig-U05079-1Q) /CSM_Contig/Conti...    36  0.014
Contig-U04560-1 (Contig-U04560-1Q) /CSM_Contig/Conti...    36  0.014
Contig-U01998-1 (Contig-U01998-1Q) /CSM_Contig/Conti...    36  0.014

>Contig-U04669-1 (Contig-U04669-1Q) /CSM_Contig/Contig-U04669-1Q.Seq.d
          Length = 208

 Score =  161 bits (81), Expect = 4e-40
 Identities = 95/102 (93%)
 Strand = Plus / Plus

                                                                       
Query: 1   ataatttcatatttttaattatatcacatcattaattattcaccaacacnnnnnnnaaaa 60
           |||||||||||||||||||||||||||||||||||||||||||||||||       ||||
Sbjct: 1   ataatttcatatttttaattatatcacatcattaattattcaccaacactttttttaaaa 60

                                                     
Query: 61  tattatcaataaaatttatgatattaatattttttttttatt 102
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tattatcaataaaatttatgatattaatattttttttttatt 102


 Score = 95.6 bits (48), Expect = 2e-20
 Identities = 48/48 (100%)
 Strand = Plus / Plus

                                                           
Query: 136 gtatacttttatatttttataaattaagatacttaaaaaataaatctt 183
           ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 136 gtatacttttatatttttataaattaagatacttaaaaaataaatctt 183


>Contig-U14535-1 (Contig-U14535-1Q) /CSM_Contig/Contig-U14535-1Q.Seq.d
          Length = 614

 Score = 38.2 bits (19), Expect = 0.004
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                              
Query: 83  attaatattttttttttat 101
           |||||||||||||||||||
Sbjct: 445 attaatattttttttttat 427


>Contig-U11335-1 (Contig-U11335-1Q) /CSM_Contig/Contig-U11335-1Q.Seq.d
          Length = 2396

 Score = 38.2 bits (19), Expect = 0.004
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                               
Query: 9    atatttttaattatatcac 27
            |||||||||||||||||||
Sbjct: 1935 atatttttaattatatcac 1953


  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: 17,773
Number of Sequences: 6905
Number of extensions: 17773
Number of successful extensions: 7226
Number of sequences better than 10.0: 722
length of query: 208
length of database: 5,674,871
effective HSP length: 15
effective length of query: 193
effective length of database: 5,571,296
effective search space: 1075260128
effective search space used: 1075260128
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 2009. 6.28
Homology vs DNA 
Query= Contig-U04669-1 (Contig-U04669-1Q) /CSM_Contig/Contig-U04669-1Q.Seq.d
         (208 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(AU071678) Dictyostelium discoideum slug cDNA, clone SSC251.       98   2e-30  2
(CD119866) ME1-0059T-M196-E01-U.G ME1-0059 Schistosoma manso...    52   0.008  1
(AX652361) Sequence 2231 from Patent WO03000898.                   36   0.015  3
(AX508964) Sequence 3659 from Patent WO0216655.                    36   0.015  3
(BZ517547) BOMSH44TF BO_2_3_KB Brassica oleracea genomic clo...    38   0.026  2
(CU694753) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    50   0.032  1
(DT603911) nad03-43ms3-d09 Nad03 Nuphar advena cDNA clone na...    50   0.032  1
(AM910995) Plasmodium knowlesi strain H chromosome 13, compl...    46   0.49   1
(AP003031) Homo sapiens genomic DNA, chromosome 11q clone:RP...    46   0.49   1
(AC021221) Homo sapiens chromosome 11 clone RP11-535A19, WOR...    46   0.49   1
(EI333354) GM_WBc0074B15.f GM_WBc Glycine max genomic clone ...    46   0.49   1
(CG770449) TcB49.1_H12_SP6 Tribolium BAC library Tribolium c...    46   0.49   1
(GD147852) CD012302 Human CD34+ ESTs from primary hematopoie...    46   0.49   1
(GD147775) CD012225 Human CD34+ ESTs from primary hematopoie...    46   0.49   1
(EK222666) 1095460146044 Global-Ocean-Sampling_GS-31-01-01-1...    34   1.3    2
(FH764248) OSB_1164004xe07r1.ab1 OSB_1164 Nicotiana tabacum ...    36   1.3    2
(FH764299) OSB_1164004xa14f1.ab1 OSB_1164 Nicotiana tabacum ...    36   1.3    2
(FH764869) OSB_1164001xm14f1.ab1 OSB_1164 Nicotiana tabacum ...    36   1.3    2
(EK201894) 1095460059047 Global-Ocean-Sampling_GS-31-01-01-1...    34   1.3    2
(FH764010) OSB_1164002xb14f1.ab1 OSB_1164 Nicotiana tabacum ...    36   1.3    2
(FH765220) OSB_1164001xp10f1.ab1 OSB_1164 Nicotiana tabacum ...    36   1.3    2
(FH764481) OSB_1164004xj01f1.ab1 OSB_1164 Nicotiana tabacum ...    36   1.4    2
(FJ497008) Latimeria menadoensis HoxD gene cluster, complete...    44   1.9    1
(AC209189) Populus trichocarpa clone POP078-I10, complete se...    44   1.9    1
(CT476832) Pig DNA sequence from clone XX-BE284E13 on chromo...    44   1.9    1
(AC141824) Apis mellifera clone CH224-62B12, *** SEQUENCING ...    44   1.9    1
(CU657960) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   1.9    1
(CT025941) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   1.9    1
(AC203110) Saimiri boliviensis boliviensis clone CH254-274N1...    44   1.9    1
(AC202635) Saimiri boliviensis boliviensis clone CH254-377E1...    44   1.9    1
(ER381735) 1094338772094 Global-Ocean-Sampling_GS-34-01-01-1...    44   1.9    1
(EK051489) 1092959706742 Global-Ocean-Sampling_GS-31-01-01-1...    44   1.9    1
(EK016394) 1092955235646 Global-Ocean-Sampling_GS-31-01-01-1...    44   1.9    1
(CW945265) TcB27.3_E11_T7 Tribolium BAC library Tribolium ca...    44   1.9    1
(CT112856) Sus scrofa genomic clone PigE-89E15, genomic surv...    44   1.9    1
(DR762019) HESC4_135_E05.g1_A037 NIH_MGC_262 Homo sapiens cD...    44   1.9    1
(GE861006) 1112870009876 BABEVCEREB-C-01-1-7KB Papio anubis ...    44   1.9    1
(FC166961) 1106908712191 BABEVPN-C-01-1-7KB Papio anubis cDN...    44   1.9    1
(CP000013) Borrelia garinii PBi, complete genome.                  44   1.9    1
(AM488641) Vitis vinifera contig VV78X229894.9, whole genome...    42   2.2    3
(Z81541) Caenorhabditis elegans Cosmid F48F5.                      36   2.6    2
(AL137069) Human DNA sequence from clone RP11-167C5 on chrom...    40   2.9    3
(AE001437) Clostridium acetobutylicum ATCC 824, complete gen...    34   3.0    2
(AL773530) Mouse DNA sequence from clone RP23-180A8 on chrom...    42   3.4    2
(CP000263) Buchnera aphidicola str. Cc (Cinara cedri), compl...    34   3.5    2
(AJ245645) Prototheca wickerhamii chloroplast partial genome.      34   3.6    3
(AM458569) Vitis vinifera contig VV78X180401.7, whole genome...    38   4.5    3
(EI880500) CAH1-66J9TR CAA1Ba Cicer arietinum genomic clone ...    38   4.8    2
(CZ501913) GMW2-14P23a.g1 GMW2 Glycine max genomic, genomic ...    34   5.0    2
(DX533921) GH_MBb0081G21r GH_MBb Gossypium hirsutum genomic ...    36   7.2    2
(AM479233) Vitis vinifera contig VV78X037493.1, whole genome...    36   7.3    2
(AC192789) Gallus gallus BAC clone CH261-36O18 from chromoso...    42   7.7    1
(AC189010) Gallus gallus BAC clone CH261-53H12 from chromoso...    42   7.7    1
(AB083042) Gallus gallus gene for ZOV3 protein, partial cds,...    42   7.7    1
(AC187574) Rhesus macaque BAC clone CH250-33H12 from chromos...    42   7.7    1
(AF446141) Aegilops tauschii LZ-NBS-LRR class RGA, NBS-LRR c...    42   7.7    1
(GC701782) Sequence 17027 from patent US 6812339.                  42   7.7    1
(GC696913) Sequence 12158 from patent US 6812339.                  42   7.7    1
(AL139004) Human DNA sequence from clone RP11-398O19 on chro...    42   7.7    1
(AC009721) Homo sapiens 12q24.1-116.6-118.9 BAC RP11-129O9 (...    42   7.7    1
(AC149445) Papio anubis clone RP41-148H18, WORKING DRAFT SEQ...    42   7.7    1
(AC129298) Mus musculus chromosome UNK clone RP24-419H23, WO...    42   7.7    1
(AC111268) Rattus norvegicus clone CH230-42E7, *** SEQUENCIN...    42   7.7    1
(AC103342) Rattus norvegicus clone CH230-1G1, *** SEQUENCING...    42   7.7    1
(AC225338) Zea mays chromosome 3 clone CH201-562A22; ZMMBBc0...    42   7.7    1
(ER861909) POTM228TR Solanum tuberosum RHPOTKEY BAC ends Sol...    42   7.7    1
(EK175114) 1095458094262 Global-Ocean-Sampling_GS-31-01-01-1...    42   7.7    1
(EJ898664) 1093018478505 Global-Ocean-Sampling_GS-30-02-01-1...    42   7.7    1
(EJ785319) 1093017311095 Global-Ocean-Sampling_GS-30-02-01-1...    42   7.7    1
(EI836953) POTI123TF Solanum tuberosum RHPOTKEY BAC ends Sol...    42   7.7    1
(EI826198) POTH132TR Solanum tuberosum RHPOTKEY BAC ends Sol...    42   7.7    1
(DX899566) KBrH031H02F KBrH, Brassica rapa HindIII BAC libra...    42   7.7    1
(DX825683) ZMMBLb0003I06.r ZMMBLb Zea mays genomic clone ZMM...    42   7.7    1
(DX470079) Cpl12110 Papaya Genomic DNA BAC Library Carica pa...    42   7.7    1
(DU903154) 417421 Tomato HindIII BAC Library Solanum lycoper...    42   7.7    1
(DU859053) 55761 Tomato HindIII BAC Library Solanum lycopers...    42   7.7    1
(DU847030) 35135 Tomato HindIII BAC Library Solanum lycopers...    42   7.7    1
(CZ815966) OC__Ba0192I13.f OC__Ba Oryza coarctata genomic cl...    42   7.7    1
(CZ719500) OC__Ba0044F24.f OC__Ba Oryza coarctata genomic cl...    42   7.7    1
(CL298972) ZMMBBb0054F18f ZMMBBb (HindIII) Zea mays subsp. m...    42   7.7    1
(BH970790) odf84d05.b1 B.oleracea002 Brassica oleracea genom...    42   7.7    1
(DW510421) GH_TMIRS_143_C12_F Cotton Normalized Library dT p...    42   7.7    1
(DW497807) GH_TMIRS_019_G12_F Cotton Normalized Library dT p...    42   7.7    1
(DT467953) GH_CHX21C24.f GH_CHX Gossypium hirsutum cDNA clon...    42   7.7    1
(DB758584) Apis mellifera head cDNA, RIKEN full-length enric...    42   7.7    1
(CU624043) Theobroma cacao, mRNA sequence (KZ0ABE13YJ12FM1).       42   7.7    1
(CU591562) Theobroma cacao, mRNA sequence (KZ0AAH11YA04FM1).       42   7.7    1
(BQ149385) NF089H06FL1F1059 Developing flower Medicago trunc...    42   7.7    1
(BG850177) 1024028B11.x1 C. reinhardtii CC-1690, normalized,...    42   7.7    1
(CP000814) Campylobacter jejuni subsp. jejuni 81116, complet...    42   7.7    1
(CP000768) Campylobacter jejuni subsp. doylei 269.97, comple...    42   7.7    1
(CP000678) Methanobrevibacter smithii ATCC 35061, complete g...    42   7.7    1
(CP000538) Campylobacter jejuni subsp. jejuni 81-176, comple...    42   7.7    1
(CP000395) Borrelia afzelii PKo, complete genome.                  42   7.7    1
(CP000025) Campylobacter jejuni RM1221, complete genome.           42   7.7    1
(AL111168) Campylobacter jejuni subsp. jejuni NCTC 11168 com...    42   7.7    1

>(AU071678) Dictyostelium discoideum slug cDNA, clone SSC251.
          Length = 209

 Score = 97.6 bits (49), Expect(2) = 2e-30
 Identities = 49/49 (100%)
 Strand = Plus / Plus


Query: 1  ataatttcatatttttaattatatcacatcattaattattcaccaacac 49
          |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  ataatttcatatttttaattatatcacatcattaattattcaccaacac 49

 Score = 65.9 bits (33), Expect(2) = 2e-30
 Identities = 33/33 (100%)
 Strand = Plus / Plus


Query: 57 aaaatattatcaataaaatttatgatattaata 89
          |||||||||||||||||||||||||||||||||
Sbjct: 57 aaaatattatcaataaaatttatgatattaata 89

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 149,725,170
Number of extensions: 11034159
Number of successful extensions: 3344712
Number of sequences better than 10.0: 98
Length of query: 208
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 185
Effective length of database: 99,442,330,388
Effective search space: 18396831121780
Effective search space used: 18396831121780
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04669-1 (Contig-U04669-1Q) /CSM_Contig/Contig-U04669-1Q.Seq.d
         (208 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 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: 3268448
Number of Hits to DB: 89,516,899
Number of extensions: 665718
Number of successful extensions: 280
Number of sequences better than 10.0: 0
Number of HSP's gapped: 280
Number of HSP's successfully gapped: 0
Length of query: 69
Length of database: 1,061,185,681
Length adjustment: 41
Effective length of query: 28
Effective length of database: 927,179,313
Effective search space: 25961020764
Effective search space used: 25961020764
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: 0.81  gvh: -0.01  alm: 0.52  top: 0.53  tms: 0.00  mit: 0.34  mip: 0.00
 nuc: 0.57  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 

	 84.0 %: nuclear
	  8.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: plasma membrane

>> prediction for Contig-U04669-1 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) 1
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