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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-U01810-1
Contig ID Contig-U01810-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01810-1 (Contig-U01810-1Q) /CSM_Contig/Contig-U01810-1Q.Seq.d
AAATGGTGAAAATGATATTTTANGAATTAATAATTCAACAACGATAACAA
GTGAACAATTTCCAAATAATAGTAAAATGATTGAATTTGGTGATGATTTC
AATGGAATTATTAATGTCGATTATATAGCTAATAAAAAGGTTGTTATTTT
AAATAATCCAAAAAAAAAAAAAAA
Gap no gap
Contig length 174
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 1139643
End point 1139483
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U01810
List of clone(s) 

est1=SSH717Z,1,175
Translated Amino Acid sequence 
NGENDILXINNSTTITSEQFPNNSKMIEFGDDFNGIINVDYIANKKVVILNNPKKKK
Translated Amino Acid sequence (All Frames) 
Frame A:
kw*k*yfxn**fnndnk*tisk***nd*iw**fqwny*crlys**kgcyfk*skkkkk


Frame B:
NGENDILXINNSTTITSEQFPNNSKMIEFGDDFNGIINVDYIANKKVVILNNPKKKK


Frame C:
mvkmifxeliiqqr*qvnnfqiivk*lnlvmismellmsii*likrllf*iiqkkkk
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01810-1 (Contig-U01810-1Q)
/CSM_Contig/Contig-U01810-1Q.Seq.d
         (174 letters)

Database: CSM
           8361 sequences; 7,895,291 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01810-1 (Contig-U01810-1Q) /CSM_Contig/Conti...   309  7e-85
Contig-U02425-1 (Contig-U02425-1Q) /CSM_Contig/Conti...    48  4e-06
Contig-U11702-1 (Contig-U11702-1Q) /CSM_Contig/Conti...    36  0.016
Contig-U10198-1 (Contig-U10198-1Q) /CSM_Contig/Conti...    36  0.016
Contig-U08780-1 (Contig-U08780-1Q) /CSM_Contig/Conti...    36  0.016
Contig-U06842-1 (Contig-U06842-1Q) /CSM_Contig/Conti...    36  0.016
Contig-U13928-1 (Contig-U13928-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U12405-1 (Contig-U12405-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U11201-1 (Contig-U11201-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U11106-1 (Contig-U11106-1Q) /CSM_Contig/Conti...    34  0.063

>Contig-U01810-1 (Contig-U01810-1Q) /CSM_Contig/Contig-U01810-1Q.Seq.d
          Length = 174

 Score =  309 bits (156), Expect = 7e-85
 Identities = 159/159 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aaatggtgaaaatgatattttangaattaataattcaacaacgataacaagtgaacaatt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaatggtgaaaatgatattttangaattaataattcaacaacgataacaagtgaacaatt 60

                                                                       
Query: 61  tccaaataatagtaaaatgattgaatttggtgatgatttcaatggaattattaatgtcga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tccaaataatagtaaaatgattgaatttggtgatgatttcaatggaattattaatgtcga 120

                                                  
Query: 121 ttatatagctaataaaaaggttgttattttaaataatcc 159
           |||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ttatatagctaataaaaaggttgttattttaaataatcc 159


>Contig-U02425-1 (Contig-U02425-1Q) /CSM_Contig/Contig-U02425-1Q.Seq.d
          Length = 1254

 Score = 48.1 bits (24), Expect = 4e-06
 Identities = 24/24 (100%)
 Strand = Plus / Plus

                                   
Query: 80  attgaatttggtgatgatttcaat 103
           ||||||||||||||||||||||||
Sbjct: 126 attgaatttggtgatgatttcaat 149


>Contig-U11702-1 (Contig-U11702-1Q) /CSM_Contig/Contig-U11702-1Q.Seq.d
          Length = 1606

 Score = 36.2 bits (18), Expect = 0.016
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 25  aattaataattcaacaac 42
           ||||||||||||||||||
Sbjct: 981 aattaataattcaacaac 998


  Database: CSM
    Posted date:  Jun 7, 2004  8:33 AM
  Number of letters in database: 7,895,291
  Number of sequences in database:  8361
  
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: 6494
Number of Sequences: 8361
Number of extensions: 6494
Number of successful extensions: 1952
Number of sequences better than 10.0: 256
length of query: 174
length of database: 7,895,291
effective HSP length: 15
effective length of query: 159
effective length of database: 7,769,876
effective search space: 1235410284
effective search space used: 1235410284
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. 5. 8
Homology vs DNA 
Query= Contig-U01810-1 (Contig-U01810-1Q) /CSM_Contig/Contig-U01810-1Q.Seq.d
         (174 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

(AU038435) Dictyostelium discoideum slug cDNA, clone SSH717.      309   2e-80  1
(AE017143) Haemophilus ducreyi strain 35000HP complete genome.     50   0.026  1
(AU061958) Dictyostelium discoideum slug cDNA, clone SLG774.       48   0.10   1
(AL596174) Listeria innocua Clip11262 complete genome, segme...    42   0.15   4
(DU042928) 159380 Tomato HindIII BAC Library Solanum lycoper...    36   0.23   2
(AX413018) Sequence 9 from Patent WO0228891.                       42   0.28   7
(FI300544) AdH1006-CPY2-K4TF AdH1 Arachis duranensis genomic...    46   0.40   1
(CU469464) Candidatus Phytoplasma mali strain AT complete ch...    32   0.85   8
(AC178404) Strongylocentrotus purpuratus clone R3-3111B03, W...    40   1.1    4
(AC005292) Genomic sequence for Arabidopsis thaliana BAC F26...    44   1.6    1
(AC002311) Arabidopsis thaliana chromosome I BAC T26J12 geno...    44   1.6    1
(AC155192) Bos taurus clone CH240-43A24, WORKING DRAFT SEQUE...    44   1.6    1
(AC166392) Bos taurus clone CH240-188H11, WORKING DRAFT SEQU...    44   1.6    1
(BH236487) AUIEB60TF AUIE Arabidopsis thaliana genomic clone...    44   1.6    1
(EJ254146) 1095347006133 Global-Ocean-Sampling_GS-27-01-01-1...    44   1.6    1
(CR401120) Arabidopsis thaliana T-DNA flanking sequence GK-8...    44   1.6    1
(CG026894) PGAAE76TR PGAA Carica papaya genomic clone PGAAE7...    44   1.6    1
(CC455823) SALK_089137.50.05.x Arabidopsis thaliana TDNA ins...    44   1.6    1
(BH901786) SALK_086457.54.10.x Arabidopsis thaliana TDNA ins...    44   1.6    1
(ES421363) pm_OSU_shoot_CA_2003-04_047A12 Douglas-fir cold a...    44   1.6    1
(CF582193) AGENCOURT_11360681_updated NIH_MGC_137 Mus muscul...    44   1.6    1
(CP000422) Pediococcus pentosaceus ATCC 25745, complete genome.    44   1.6    1
(AM448765) Vitis vinifera contig VV78X229367.3, whole genome...    40   2.1    2
(AX417049) Sequence 4040 from Patent WO0228891.                    42   2.6    4
(AC172380) Strongylocentrotus purpuratus clone R3-1004L22, W...    40   3.1    3
(CZ541604) SRAA-aad39c08.g1 Strongyloides ratti whole genome...    34   3.6    3
(EK517664) 1095515505718 Global-Ocean-Sampling_GS-32-01-01-1...    36   3.8    2
(CR388212) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    32   4.2    6
(GH727918) G608.111A19F010911 G608 Triticum aestivum cDNA cl...    32   4.2    2
(AP010074) Lotus japonicus genomic DNA, chromosome 1, clone:...    36   5.5    4
(DL081580) Listeria innocua, genome and applications.              42   5.5    7
(AM476110) Vitis vinifera contig VV78X267385.15, whole genom...    40   5.7    2
(Z81104) Caenorhabditis elegans Cosmid M199.                       38   6.2    4
(CU104738) Mouse DNA sequence from clone WI1-2791P21 on chro...    42   6.3    1
(AL607088) Mouse DNA sequence from clone RP23-13A13 on chrom...    42   6.3    1
(AM489399) Vitis vinifera, whole genome shotgun sequence, co...    42   6.3    1
(AM459625) Vitis vinifera, whole genome shotgun sequence, co...    42   6.3    1
(DL083629) Listeria innocua, genome and applications.              42   6.3    1
(AX417036) Sequence 4027 from Patent WO0228891.                    42   6.3    1
(AY923052) Homo sapiens PDZ and LIM domain 1 (elfin) (PDLIM1...    42   6.3    1
(AL157834) Human DNA sequence from clone RP11-310E22 on chro...    42   6.3    1
(AC084198) Homo sapiens 3 BAC RP11-454H13 (Roswell Park Canc...    42   6.3    1
(AC006305) Homo sapiens chromosome 18, clone RP11-456O19, co...    42   6.3    1
(FJ429368) Carica papaya clone 55E02, *** SEQUENCING IN PROG...    42   6.3    1
(AC090758) Homo sapiens chromosome 18 clone RP11-822F4 map 1...    42   6.3    1
(AP002786) Homo sapiens genomic DNA, chromosome 18q21 clone:...    42   6.3    1
(AC232474) Brassica rapa subsp. pekinensis clone KBrB027P21,...    42   6.3    1
(AC173540) Bos taurus clone CH240-68F9, WORKING DRAFT SEQUEN...    42   6.3    1
(AC023292) Homo sapiens clone RP11-16M4, WORKING DRAFT SEQUE...    42   6.3    1
(AC023071) Homo sapiens chromosome 3 clone RP11-423D7 map 3,...    42   6.3    1
(AC021467) Homo sapiens clone RP11-387C17, WORKING DRAFT SEQ...    42   6.3    1
(FH309546) CHO_OF4424xe05f1.ab1 CHO_OF4 Nicotiana tabacum ge...    42   6.3    1
(ER410988) 1095370004188 Global-Ocean-Sampling_GS-34-01-01-1...    42   6.3    1
(ER368031) 1093022128339 Global-Ocean-Sampling_GS-34-01-01-1...    42   6.3    1
(EJ483220) 1095403483179 Global-Ocean-Sampling_GS-28-01-01-1...    42   6.3    1
(EJ075647) 1095458120207 Global-Ocean-Sampling_GS-26-01-01-1...    42   6.3    1
(EJ055760) 1095456027043 Global-Ocean-Sampling_GS-26-01-01-1...    42   6.3    1
(DU372890) 1098312004164 CHORI-243 Ovis aries genomic clone ...    42   6.3    1
(DU177160) 1098553468643 CHORI-243 Ovis aries genomic clone ...    42   6.3    1
(CR863791) Sus scrofa BES.                                         42   6.3    1
(CG751606) P046-1-C11.za Ppa EcoRI BAC Library Pristionchus ...    42   6.3    1
(DY324367) OB_EEa06D05.r OB_EEa Ocimum basilicum cDNA clone ...    42   6.3    1
(DY324366) OB_EEa06D05.f OB_EEa Ocimum basilicum cDNA clone ...    42   6.3    1
(BQ444152) UI-M-EX0-bxj-f-04-0-UI.r1 NIH_BMAP_EX0 Mus muscul...    42   6.3    1
(FG541645) OtP011B11_013007d Onthophagus taurus pupal librar...    42   6.3    1
(CG813791) SOYAU42TV LargeInsertSoybeanGenLib Glycine max ge...    32   7.0    2
(AC210233) Zea mays chromosome 9 clone ZMMBBb-574N21; ZMMBBb...    40   7.9    2
(AC116957) Dictyostelium discoideum chromosome 2 map 1685067...    30   9.5    9
(EJ271218) 1095353016871 Global-Ocean-Sampling_GS-27-01-01-1...    34   10.0   2

>(AU038435) Dictyostelium discoideum slug cDNA, clone SSH717.
          Length = 175

 Score =  309 bits (156), Expect = 2e-80
 Identities = 159/159 (100%)
 Strand = Plus / Plus


Query: 1   aaatggtgaaaatgatattttangaattaataattcaacaacgataacaagtgaacaatt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaatggtgaaaatgatattttangaattaataattcaacaacgataacaagtgaacaatt 60


Query: 61  tccaaataatagtaaaatgattgaatttggtgatgatttcaatggaattattaatgtcga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tccaaataatagtaaaatgattgaatttggtgatgatttcaatggaattattaatgtcga 120


Query: 121 ttatatagctaataaaaaggttgttattttaaataatcc 159
           |||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ttatatagctaataaaaaggttgttattttaaataatcc 159

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 239,682,880
Number of extensions: 14823365
Number of successful extensions: 4184262
Number of sequences better than 10.0: 71
Length of query: 174
Length of database: 101,790,757,118
Length adjustment: 22
Effective length of query: 152
Effective length of database: 99,544,435,898
Effective search space: 15130754256496
Effective search space used: 15130754256496
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01810-1 (Contig-U01810-1Q) /CSM_Contig/Contig-U01810-1Q.Seq.d
         (174 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CR378673_35(CR378673|pid:none) Photobacterium profundum SS9; seg...    32   5.3
(Q5UPL6) RecName: Full=Putative BTB/POZ domain and WD-repeat pro...    32   5.3
CP000361_1197(CP000361|pid:none) Arcobacter butzleri RM4018, com...    32   6.9
CP000609_614(CP000609|pid:none) Methanococcus maripaludis C5, co...    32   9.0

>CR378673_35(CR378673|pid:none) Photobacterium profundum SS9;
           segment 11/12.
          Length = 301

 Score = 32.3 bits (72), Expect = 5.3
 Identities = 20/46 (43%), Positives = 26/46 (56%)
 Frame = +2

Query: 35  STTITSEQFPNNSKMIEFGDDFNGIINVDYIANKKVVILNNPKKKK 172
           S T+  E+F  N KM  F  D NG+I V+    KK+VI  N +K K
Sbjct: 212 SVTVEIERFDYNPKMDGF--DINGLIFVERKGQKKMVIGKNGEKMK 255

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: 210,321,642
Number of extensions: 3228859
Number of successful extensions: 5955
Number of sequences better than 10.0: 4
Number of HSP's gapped: 5949
Number of HSP's successfully gapped: 4
Length of query: 58
Length of database: 1,051,180,864
Length adjustment: 31
Effective length of query: 27
Effective length of database: 950,847,535
Effective search space: 25672883445
Effective search space used: 25672883445
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: 0.75  gvh: 0.38  alm: 0.49  top: 0.53  tms: 0.00  mit: 0.15  mip: 0.00
 nuc: 0.07  erl: 0.00  erm: 0.60  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 %: nuclear
	 40.0 %: cytoplasmic
	  4.0 %: vacuolar
	  4.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U01810-1 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