NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U04194-1
Contig ID Contig-U04194-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04194-1 (Contig-U04194-1Q) /CSM_Contig/Contig-U04194-1Q.Seq.d
ATTTTATATTTAATATATGTCCATACTTAATCAGACTAAAAGACTGAGGA
TTATATTATCGTAAGCACCTCCTTCATGCACGATATAGCCAAGTTGGTAA
GGCGATGGTTTTTGATATCATCACGCGTAGGTTCGAGTCCTACTATCGGA
AAATTGGATTTATGGGACTTAAAAATCTATTGAATATTTTCCCATATATT
TTTCCTAATAGTTATATTATAGTATAATAAGAACTTCAAATCGCAGTTGT
TCTATAAAACGATTAGTTCTTATTAGATATTTTTAAGTCACCTGTTGT
Gap no gap
Contig length 298
Chromosome number (1..6, M) M
Chromosome length 55569
Start point 22794
End point 23014
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 2
Link to clone list U04194
List of clone(s) 

est1=SLH676E,1,299
est2=SLH631E,2,299
Translated Amino Acid sequence 
fifnicpylirlkd*GLYYRKHLLHARYSQVGKAMVFDIITRRFESYYRKIGFMGLKNLL
NIFPYIFPNSYIIV**elqiavvl*nd*flldifkspv
Translated Amino Acid sequence (All Frames) 
Frame A:
ilyliyvht*sd*ktedyiivstsfmhdiaklvrrwflissrvgssptigkldlwdlkiy
*ifshifflivil*ynknfksqlfyktissy*iflshll


Frame B:
fyi*ymsilnqtkrlriils*appscti*psw*gdgf*yhha*vrvllsenwiygt*ksi
eyfpiyfs**lyysiirtsnrscsikrlvliryf*vtcc


Frame C:
fifnicpylirlkd*GLYYRKHLLHARYSQVGKAMVFDIITRRFESYYRKIGFMGLKNLL
NIFPYIFPNSYIIV**elqiavvl*nd*flldifkspv
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U04194-1 (Contig-U04194-1Q)
/CSM_Contig/Contig-U04194-1Q.Seq.d
         (298 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04194-1 (Contig-U04194-1Q) /CSM_Contig/Conti...   591  e-169
Contig-U11260-1 (Contig-U11260-1Q) /CSM_Contig/Conti...    34  0.080
Contig-U13885-1 (Contig-U13885-1Q) /CSM_Contig/Conti...    32  0.32
Contig-U13841-1 (Contig-U13841-1Q) /CSM_Contig/Conti...    32  0.32
Contig-U12301-1 (Contig-U12301-1Q) /CSM_Contig/Conti...    32  0.32
Contig-U14729-1 (Contig-U14729-1Q) /CSM_Contig/Conti...    30  1.3
Contig-U11366-1 (Contig-U11366-1Q) /CSM_Contig/Conti...    30  1.3
Contig-U11287-1 (Contig-U11287-1Q) /CSM_Contig/Conti...    30  1.3
Contig-U10996-1 (Contig-U10996-1Q) /CSM_Contig/Conti...    30  1.3
Contig-U09934-1 (Contig-U09934-1Q) /CSM_Contig/Conti...    30  1.3

>Contig-U04194-1 (Contig-U04194-1Q) /CSM_Contig/Contig-U04194-1Q.Seq.d
          Length = 298

 Score =  591 bits (298), Expect = e-169
 Identities = 298/298 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   attttatatttaatatatgtccatacttaatcagactaaaagactgaggattatattatc 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   attttatatttaatatatgtccatacttaatcagactaaaagactgaggattatattatc 60

                                                                       
Query: 61  gtaagcacctccttcatgcacgatatagccaagttggtaaggcgatggtttttgatatca 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gtaagcacctccttcatgcacgatatagccaagttggtaaggcgatggtttttgatatca 120

                                                                       
Query: 121 tcacgcgtaggttcgagtcctactatcggaaaattggatttatgggacttaaaaatctat 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tcacgcgtaggttcgagtcctactatcggaaaattggatttatgggacttaaaaatctat 180

                                                                       
Query: 181 tgaatattttcccatatatttttcctaatagttatattatagtataataagaacttcaaa 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tgaatattttcccatatatttttcctaatagttatattatagtataataagaacttcaaa 240

                                                                     
Query: 241 tcgcagttgttctataaaacgattagttcttattagatatttttaagtcacctgttgt 298
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tcgcagttgttctataaaacgattagttcttattagatatttttaagtcacctgttgt 298


>Contig-U11260-1 (Contig-U11260-1Q) /CSM_Contig/Contig-U11260-1Q.Seq.d
          Length = 1344

 Score = 34.2 bits (17), Expect = 0.080
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 4   ttatatttaatatatgt 20
           |||||||||||||||||
Sbjct: 125 ttatatttaatatatgt 109


>Contig-U13885-1 (Contig-U13885-1Q) /CSM_Contig/Contig-U13885-1Q.Seq.d
          Length = 1396

 Score = 32.2 bits (16), Expect = 0.32
 Identities = 19/20 (95%)
 Strand = Plus / Minus

                               
Query: 104 gatggtttttgatatcatca 123
           ||||||||||| ||||||||
Sbjct: 846 gatggtttttgttatcatca 827


  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: 2456
Number of Sequences: 6905
Number of extensions: 2456
Number of successful extensions: 761
Number of sequences better than 10.0: 61
length of query: 298
length of database: 5,674,871
effective HSP length: 15
effective length of query: 283
effective length of database: 5,571,296
effective search space: 1576676768
effective search space used: 1576676768
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. 6.14
Homology vs DNA 
Query= Contig-U04194-1 (Contig-U04194-1Q) /CSM_Contig/Contig-U04194-1Q.Seq.d
         (298 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

(AU039380) Dictyostelium discoideum slug cDNA, clone SLH676.      591   e-165  1
(AU039358) Dictyostelium discoideum slug cDNA, clone SLH631.      589   e-164  1
(D16466) Dictyostelium discoideum mitochondrial genes for la...   313   2e-81  1
(AB000109) Dictyostelium discoideum mitochondrial DNA, compl...   313   2e-81  1
(DQ336395) Dictyostelium citrinum mitochondrion, complete ge...   137   3e-28  1
(D61390) Dictyostelium mucoroides mitochondrial DNA, large s...    62   1e-05  1
(CP001103) Alteromonas macleodii 'Deep ecotype', complete ge...    40   0.002  2
(EK537562) 1095516039091 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK477319) 1095469492824 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK581401) 1095521701811 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK490663) 1095505080656 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK552795) 1095516124626 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK450585) 1095467259028 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK492697) 1095505097682 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK510771) 1095515475934 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EK446062) 1095467041067 Global-Ocean-Sampling_GS-32-01-01-1...    40   0.003  2
(EU760701) Volvox carteri f. nagariensis strain HK10 mitocho...    40   0.009  2
(CP000724) Alkaliphilus metalliredigens QYMF, complete genome.     36   0.092  2
(CP000853) Alkaliphilus oremlandii OhILAs, complete genome.        36   0.095  2
(AF404303) Spizellomyces punctatus mitochondrial chromosome ...    48   0.19   1
(AF295546) Malawimonas jakobiformis mitochondrial DNA, compl...    44   0.27   3
(EU651892) Hemiselmis andersenii strain CCMP 644 mitochondri...    46   0.73   1
(CW609808) OA_ABa0150P02.r OA_ABa Oryza australiensis genomi...    46   0.73   1
(CL918978) OA_ABa0022M07.f OA_ABa Oryza australiensis genomi...    46   0.73   1
(AP008207) Oryza sativa (japonica cultivar-group) genomic DN...    32   1.0    2
(AF538045) Amoebidium parasiticum mitochondrial chromosome 2...    36   1.1    2
(AC096517) Rattus norvegicus clone CH230-16H15, WORKING DRAF...    38   1.3    4
(AP003344) Oryza sativa Japonica Group genomic DNA, chromoso...    32   1.5    2
(DB769940) Apis mellifera head cDNA, RIKEN full-length enric...    38   1.5    2
(EU912438) Vaucheria litorea chloroplast, complete genome.         32   1.6    5
(DB780677) Apis mellifera head cDNA, RIKEN full-length enric...    38   1.7    2
(DB771879) Apis mellifera head cDNA, RIKEN full-length enric...    38   1.7    2
(DB757767) Apis mellifera head cDNA, RIKEN full-length enric...    38   1.7    2
(EA702786) Sequence 81665 from patent US 7365185.                  32   1.7    2
(DB757255) Apis mellifera head cDNA, RIKEN full-length enric...    38   1.7    2
(DQ186202) Thalassiosira pseudonana mitochondrion, complete ...    42   2.0    2
(AC096425) Rattus norvegicus clone CH230-149B9, WORKING DRAF...    42   2.3    2
(CP000485) Bacillus thuringiensis str. Al Hakam, complete ge...    40   2.4    11
(AC161244) Mus musculus BAC clone RP24-393O16 from chromosom...    34   2.6    6
(EK937553) 1093018382621 Global-Ocean-Sampling_GS-33-01-01-1...    40   2.8    2
(AC006582) Pan troglodytes 12cp12 BAC RPCI43-77C18 (Roswell ...    34   2.8    3
(BX119922) Zebrafish DNA sequence from clone CH211-272D23 in...    44   2.9    1
(EZ035228) TSA: Acropora millepora SeqIndex66935, mRNA seque...    44   2.9    1
(EU115588) Dictyostelium discoideum Ddi2269 RNA, complete se...    44   2.9    1
(CU407196) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   2.9    1
(AC201733) Spermophilus tridecemlineatus clone VMRC20-30K21,...    44   2.9    1
(AC192322) Spermophilus tridecemlineatus clone VMRC20-373E3,...    44   2.9    1
(BH465511) BOGCY92TR BOGC Brassica oleracea genomic clone BO...    44   2.9    1
(ER540347) 1093016034593 Global-Ocean-Sampling_GS-35-01-01-1...    44   2.9    1
(DX914801) gSpTor-721.bT7 Spironucleus Zap GSS Library Spiro...    44   2.9    1
(DY613410) IMMUNEF045815C5 POSSUM_01-C-POSSUM-IMMUNE-2KB Tri...    44   2.9    1
(DY590767) GUTF074984M23 POSSUM_01-POSSUM-GUT-2KB Trichosuru...    44   2.9    1
(BY716599) Mus musculus adult male testis cDNA, RIKEN full-l...    44   2.9    1
(K00184) Bacteriophage T4 Gln-tRNA.                                36   3.2    2
(AC165368) Mus musculus BAC clone RP23-28L24 from chromosome...    34   3.7    5
(AC023355) Homo sapiens chromosome 15 clone RP11-154J22 map ...    42   3.7    4
(AC087739) Homo sapiens chromosome 15 clone RP11-154J22 map ...    42   3.8    4
(AC185683) Bos taurus clone RP42-124J1, WORKING DRAFT SEQUENCE.    40   4.3    3
(AL034557) Plasmodium falciparum MAL4P1.                           36   5.1    5
(AE017355) Bacillus thuringiensis serovar konkukian str. 97-...    40   6.1    11
(AJ010592) Guillardia theta DNA for complete sequence of nuc...    34   6.4    5
(DQ198694) Malthodes sp. UPOL 000M21 16S ribosomal RNA gene,...    32   6.6    2
(AC133602) Mus musculus BAC clone RP24-255I9 from chromosome...    42   7.0    3
(EI037535) hha0002da03.g1 hha Oryza australiensis genomic cl...    32   7.3    2
(CW595411) OA_ABa0131C15.f OA_ABa Oryza australiensis genomi...    32   7.3    2
(CU467009) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    40   7.5    2
(K00186) bacteriophage t4 gln-leu trna dimeric precursor.          36   7.9    2
(AY500367) Desmarestia viridis mitochondrion, complete genome.     38   8.0    3
(CU972379) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    34   8.2    4
(CU929533) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    34   8.6    3
(CU240296) Equus caballus GSS, BAC clone CH241-385P1, T7 end...    32   8.9    2
(FP102083) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   9.1    3
(AC123118) Rattus norvegicus clone CH230-168O8, *** SEQUENCI...    34   9.2    4
(BH453296) BOHQA24TR BOHQ Brassica oleracea genomic clone BO...    36   9.3    2
(AC219504) Bos taurus clone CH240-331M20, WORKING DRAFT SEQU...    40   9.3    3
(CP000395) Borrelia afzelii PKo, complete genome.                  38   9.5    6
(EJ338240) 1092963496318 Global-Ocean-Sampling_GS-28-01-01-1...    34   9.8    2
(CS452625) Sequence 25 from Patent WO2006119494.                   42   9.9    3
(AC084758) Homo sapiens chromosome 15 clone RP11-348A14 map ...    42   9.9    3
(CP001033) Streptococcus pneumoniae CGSP14, complete genome.       38   10.0   6

>(AU039380) Dictyostelium discoideum slug cDNA, clone SLH676.
          Length = 299

 Score =  591 bits (298), Expect = e-165
 Identities = 298/298 (100%)
 Strand = Plus / Plus


Query: 1   attttatatttaatatatgtccatacttaatcagactaaaagactgaggattatattatc 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   attttatatttaatatatgtccatacttaatcagactaaaagactgaggattatattatc 60


Query: 61  gtaagcacctccttcatgcacgatatagccaagttggtaaggcgatggtttttgatatca 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gtaagcacctccttcatgcacgatatagccaagttggtaaggcgatggtttttgatatca 120


Query: 121 tcacgcgtaggttcgagtcctactatcggaaaattggatttatgggacttaaaaatctat 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tcacgcgtaggttcgagtcctactatcggaaaattggatttatgggacttaaaaatctat 180


Query: 181 tgaatattttcccatatatttttcctaatagttatattatagtataataagaacttcaaa 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tgaatattttcccatatatttttcctaatagttatattatagtataataagaacttcaaa 240


Query: 241 tcgcagttgttctataaaacgattagttcttattagatatttttaagtcacctgttgt 298
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tcgcagttgttctataaaacgattagttcttattagatatttttaagtcacctgttgt 298

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 352,840,200
Number of extensions: 20154173
Number of successful extensions: 1792421
Number of sequences better than 10.0: 81
Length of query: 298
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 275
Effective length of database: 99,442,330,388
Effective search space: 27346640856700
Effective search space used: 27346640856700
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.29
Homology vs Protein 
Query= Contig-U04194-1 (Contig-U04194-1Q) /CSM_Contig/Contig-U04194-1Q.Seq.d
         (298 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

FN313899_1(FN313899|pid:none) Schistosoma japonicum isolate Anhu...    32   6.9
AY217827_1(AY217827|pid:none) Scelotes anguina isolate S20 cytoc...    32   7.0
AY254887_1(AY254887|pid:none) Lagidium viscacia perlutea LCM 234...    32   9.1
DQ006235_1(DQ006235|pid:none) Rana nigromaculata haplotype CX2 c...    32   9.1

>FN313899_1(FN313899|pid:none) Schistosoma japonicum isolate Anhui
           full length mRNA clone SJFCA0542|FSA001-P00029-B13,
           complete sequence.
          Length = 379

 Score = 32.0 bits (71), Expect = 6.9
 Identities = 23/80 (28%), Positives = 37/80 (46%)
 Frame = +1

Query: 58  IVSTSFMHDIAKLVRRWFLISSRVGSSPTIGKLDLWDLKIY*IFSHIFFLIVIL*YNKNF 237
           I    F HD+  ++ RW  I  R+ +      L LW+  +  +    F  IV L + K+
Sbjct: 3   IAHEKFFHDVHSVLSRWEFIILRIQT------LLLWERVVPSLVFTAFVHIVFLSFVKSS 56

Query: 238 KSQLFYKTISSY*IFLSHLL 297
            S LF   ++ + I L +LL
Sbjct: 57  LSTLFISCLALFLILLCNLL 76

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: 461,503,859
Number of extensions: 8455294
Number of successful extensions: 15168
Number of sequences better than 10.0: 4
Number of HSP's gapped: 15168
Number of HSP's successfully gapped: 4
Length of query: 99
Length of database: 1,061,185,681
Length adjustment: 68
Effective length of query: 31
Effective length of database: 838,931,217
Effective search space: 26006867727
Effective search space used: 26006867727
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: 28 (15.4 bits)
PSORT 

 psg: 0.64  gvh: 0.41  alm: 0.41  top: 0.53  tms: 0.00  mit: 0.34  mip: 0.03
 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 

	 32.0 %: cytoplasmic
	 28.0 %: mitochondrial
	 24.0 %: nuclear
	  4.0 %: extracellular, including cell wall
	  4.0 %: vacuolar
	  4.0 %: plasma membrane
	  4.0 %: peroxisomal

>> prediction for Contig-U04194-1 is cyt
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 2
SS (DIR, S) 0
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