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-U04080-1
Contig ID Contig-U04080-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U04080-1 (Contig-U04080-1Q) /CSM_Contig/Contig-U04080-1Q.Seq.d
CCCGTCACNGATTTTCGTNTTGGGNCAAATNGTNTCNCTTTNGANGANGG
TAACTTGGATTTCNCNGNTAAGGAAAANCCCAANTTGGANGGGAANCAAN
GGGANGNCAAANGCCAANGGNTTNTTGAAANCAANGANTGGGAAANTGCN
CAATTTAAAAAAGTNGNTGNTGCTAAATTTGGTTNCNGNTGGAATTNTTG
TGGTAATTNTTGGGAAGAANGGGANGAANGGNTTAAANCCNCNGCTTCAA
ATTATTAAAANCNTTAATAATTTTAATATTTTAATNGTAANCAATTTNTT
CATTCAATTNCCGNTGTTNTTAATTAATNTTTAATTAAAAAAAAAAAAAA
AAANCAAAAAATTAAAAANTATTAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 419
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 U04080
List of clone(s) 

est1=SLF279Z,1,420
Translated Amino Acid sequence 
PSXIFVLGQXVSLXXXVTWISXXRKXPXWXGXXGXXXAXGXLKXXXGKXXNLKKXXXLNL
VXXGIXVVIXGKXGXXGLXPXLQIIKXXNNFNILXVXNXFIQXPXXLINX*lkkkkkxkk
lkxikkkkkkkkkkkkkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
pvtdfrxgxnxxxxxxgnldfxxkexpxlxgxqxxxkxqxxxexxxwexaqfkkvxxakf
gxxwnxcgnxweexxexxkxxasny*xx**f*yfnxxqfxhsixxvxn*xlikkkkkxqk
ikxy*kkkkkkkkkkkkkk


Frame B:
PSXIFVLGQXVSLXXXVTWISXXRKXPXWXGXXGXXXAXGXLKXXXGKXXNLKKXXXLNL
VXXGIXVVIXGKXGXXGLXPXLQIIKXXNNFNILXVXNXFIQXPXXLINX*lkkkkkxkk
lkxikkkkkkkkkkkkkkk


Frame C:
rhxfsxwxkxxxfxxx*lgfxx*gkxqxgxexxgxqxpxxx*xqxxgxcxi*ksxxc*iw
xxxexlw*xlgrxgxxx*xxxfkllkxliilif*x*xixsfnxrcx*lxfn*kkkkkxkn
*kxlkkkkkkkkkkkkkkk
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U04080-1 (Contig-U04080-1Q)
/CSM_Contig/Contig-U04080-1Q.Seq.d
         (419 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04080-1 (Contig-U04080-1Q) /CSM_Contig/Conti...   357  6e-99
Contig-U10135-1 (Contig-U10135-1Q) /CSM_Contig/Conti...   188  3e-48
Contig-U11213-1 (Contig-U11213-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U14244-1 (Contig-U14244-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U08850-1 (Contig-U08850-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U13390-1 (Contig-U13390-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U11711-1 (Contig-U11711-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U10909-1 (Contig-U10909-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U09585-1 (Contig-U09585-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U05254-1 (Contig-U05254-1Q) /CSM_Contig/Conti...    34  0.11

>Contig-U04080-1 (Contig-U04080-1Q) /CSM_Contig/Contig-U04080-1Q.Seq.d
          Length = 419

 Score =  357 bits (180), Expect = 6e-99
 Identities = 336/336 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   cccgtcacngattttcgtnttgggncaaatngtntcnctttnganganggtaacttggat 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   cccgtcacngattttcgtnttgggncaaatngtntcnctttnganganggtaacttggat 60

                                                                       
Query: 61  ttcncngntaaggaaaancccaanttggangggaancaangggangncaaangccaangg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  ttcncngntaaggaaaancccaanttggangggaancaangggangncaaangccaangg 120

                                                                       
Query: 121 nttnttgaaancaangantgggaaantgcncaatttaaaaaagtngntgntgctaaattt 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 nttnttgaaancaangantgggaaantgcncaatttaaaaaagtngntgntgctaaattt 180

                                                                       
Query: 181 ggttncngntggaattnttgtggtaattnttgggaagaangggangaanggnttaaancc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ggttncngntggaattnttgtggtaattnttgggaagaangggangaanggnttaaancc 240

                                                                       
Query: 241 ncngcttcaaattattaaaancnttaataattttaatattttaatngtaancaatttntt 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 ncngcttcaaattattaaaancnttaataattttaatattttaatngtaancaatttntt 300

                                               
Query: 301 cattcaattnccgntgttnttaattaatntttaatt 336
           ||||||||||||||||||||||||||||||||||||
Sbjct: 301 cattcaattnccgntgttnttaattaatntttaatt 336


>Contig-U10135-1 (Contig-U10135-1Q) /CSM_Contig/Contig-U10135-1Q.Seq.d
          Length = 1395

 Score =  188 bits (95), Expect = 3e-48
 Identities = 169/203 (83%)
 Strand = Plus / Plus

                                                                        
Query: 126  tgaaancaangantgggaaantgcncaatttaaaaaagtngntgntgctaaatttggttn 185
            ||||| ||| || ||||||| ||| |||||||||||||| | || |||||||||||||| 
Sbjct: 1103 tgaaaacaaagaatgggaaactgctcaatttaaaaaagtcgctgatgctaaatttggtta 1162

                                                                        
Query: 186  cngntggaattnttgtggtaattnttgggaagaangggangaanggnttaaanccncngc 245
            | | ||||||| ||||||||||| |||||||||| | || ||| |  ||||| |  | ||
Sbjct: 1163 cagatggaattattgtggtaattattgggaagaaagagaagaaagagttaaagcagcagc 1222

                                                                        
Query: 246  ttcaaattattaaaancnttaataattttaatattttaatngtaancaatttnttcattc 305
            ||||||||| ||||| |  |||||||| |||||||||||| |||| |||||| |||||||
Sbjct: 1223 ttcaaattaataaaaacaataataattataatattttaatcgtaaacaatttattcattc 1282

                                   
Query: 306  aattnccgntgttnttaattaat 328
            |||| ||| |||| |||||||||
Sbjct: 1283 aatttccgctgttattaattaat 1305


>Contig-U11213-1 (Contig-U11213-1Q) /CSM_Contig/Contig-U11213-1Q.Seq.d
          Length = 1260

 Score = 40.1 bits (20), Expect = 0.002
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                               
Query: 264 ttaataattttaatatttta 283
           ||||||||||||||||||||
Sbjct: 51  ttaataattttaatatttta 32


  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: 3396
Number of Sequences: 6905
Number of extensions: 3396
Number of successful extensions: 334
Number of sequences better than 10.0: 128
length of query: 419
length of database: 5,674,871
effective HSP length: 16
effective length of query: 403
effective length of database: 5,564,391
effective search space: 2242449573
effective search space used: 2242449573
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. 6.13
Homology vs DNA 
Query= Contig-U04080-1 (Contig-U04080-1Q) /CSM_Contig/Contig-U04080-1Q.Seq.d
         (419 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

(AU052891) Dictyostelium discoideum slug cDNA, clone SLF279.      357   2e-94  1
(AU269442) Dictyostelium discoideum vegetative cDNA clone:VS...   188   1e-43  1
(C93251) Dictyostelium discoideum slug cDNA, clone SSM876.        188   1e-43  1
(BJ398596) Dictyostelium discoideum cDNA clone:dds1l02, 3' e...   161   3e-35  1
(C93999) Dictyostelium discoideum slug cDNA, clone SSK681.        155   2e-33  1
(AU269443) Dictyostelium discoideum vegetative cDNA clone:VS...   137   4e-28  1
(BJ436053) Dictyostelium discoideum cDNA clone:ddv29o15, 3' ...   107   8e-20  2
(BJ444483) Dictyostelium discoideum cDNA clone:ddv56c16, 3' ...   103   5e-18  1
(AU262729) Dictyostelium discoideum vegetative cDNA clone:VS...    94   5e-15  1
(BV000594) S210P6065RD4.T0 BALB/cByJ Mus musculus STS genomi...    44   4.2    1
(AC134844) Mus musculus BAC clone RP24-398A1 from chromosome...    44   4.2    1
(AM435365) Vitis vinifera contig VV78X099684.27, whole genom...    44   4.2    1
(AE016821) Ashbya gossypii (= Eremothecium gossypii) ATCC 10...    44   4.2    1
(AC189553) Brassica rapa subsp. pekinensis clone KBrH006A08,...    44   4.2    1
(AC116956) Dictyostelium discoideum chromosome 2 map 1418423...    44   4.2    1
(AC226703) Oryza minuta clone OM__Ba0015G19, *** SEQUENCING ...    44   4.2    1
(AC168733) Strongylocentrotus purpuratus clone R3-3010H21, W...    44   4.2    1
(BH124701) RPCI-24-241L2.TV RPCI-24 Mus musculus genomic clo...    44   4.2    1
(EI460215) PV_GBa0063G18.f PV_GBa Phaseolus vulgaris genomic...    44   4.2    1
(EI460191) PV_GBa0063G06.f PV_GBa Phaseolus vulgaris genomic...    44   4.2    1
(EI439024) PV_GBa0034A22.r PV_GBa Phaseolus vulgaris genomic...    44   4.2    1
(CZ937416) 257018 Tomato EcoRI BAC Library Solanum lycopersi...    44   4.2    1
(CR221752) Reverse strand read from insert in 5'HPRT inserti...    44   4.2    1
(CR101103) Reverse strand read from insert in 5'HPRT inserti...    44   4.2    1
(EC391506) CcLS1a72c20f1 Carp skin library 1 Cyprinus carpio...    44   4.2    1
(EY503114) CBBP6746.rev CBBP Hirudo medicinalis hermaphrodit...    44   4.2    1
(ES815040) UFL_269_86 Cotton fiber 0-10 day post anthesis Go...    44   4.2    1
(AM486777) Vitis vinifera contig VV78X079882.11, whole genom...    32   8.7    2
(AM475266) Vitis vinifera contig VV78X110268.7, whole genome...    32   9.0    2

>(AU052891) Dictyostelium discoideum slug cDNA, clone SLF279.
          Length = 420

 Score =  357 bits (180), Expect = 2e-94
 Identities = 336/336 (100%)
 Strand = Plus / Plus


Query: 1   cccgtcacngattttcgtnttgggncaaatngtntcnctttnganganggtaacttggat 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   cccgtcacngattttcgtnttgggncaaatngtntcnctttnganganggtaacttggat 60


Query: 61  ttcncngntaaggaaaancccaanttggangggaancaangggangncaaangccaangg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  ttcncngntaaggaaaancccaanttggangggaancaangggangncaaangccaangg 120


Query: 121 nttnttgaaancaangantgggaaantgcncaatttaaaaaagtngntgntgctaaattt 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 nttnttgaaancaangantgggaaantgcncaatttaaaaaagtngntgntgctaaattt 180


Query: 181 ggttncngntggaattnttgtggtaattnttgggaagaangggangaanggnttaaancc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ggttncngntggaattnttgtggtaattnttgggaagaangggangaanggnttaaancc 240


Query: 241 ncngcttcaaattattaaaancnttaataattttaatattttaatngtaancaatttntt 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 ncngcttcaaattattaaaancnttaataattttaatattttaatngtaancaatttntt 300


Query: 301 cattcaattnccgntgttnttaattaatntttaatt 336
           ||||||||||||||||||||||||||||||||||||
Sbjct: 301 cattcaattnccgntgttnttaattaatntttaatt 336

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 155,972,023
Number of extensions: 11733573
Number of successful extensions: 766488
Number of sequences better than 10.0: 29
Length of query: 419
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 396
Effective length of database: 99,442,330,388
Effective search space: 39379162833648
Effective search space used: 39379162833648
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.29
Homology vs Protein 
Query= Contig-U04080-1 (Contig-U04080-1Q) /CSM_Contig/Contig-U04080-1Q.Seq.d
         (419 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54QP6) RecName: Full=Oxysterol-binding protein 8; AltName: Ful...    77   2e-13

>(Q54QP6) RecName: Full=Oxysterol-binding protein 8; AltName:
           Full=OSBPh;
          Length = 402

 Score = 76.6 bits (187), Expect = 2e-13
 Identities = 41/84 (48%), Positives = 42/84 (50%)
 Frame = +1

Query: 1   PVTDFRXGXNXXXXXXGNLDFXXKEXPXLXGXQXXXKXQXXXEXXXWEXAQFKKVXXAKF 180
           PVTD R   +      GNLD   KE   L   Q   K Q   E   WE AQFKKV  AKF
Sbjct: 319 PVTDSRLRADRIALEEGNLDVAAKEKHNLEEKQREDKRQRVAENKEWETAQFKKVDDAKF 378

Query: 181 GXXWNXCGNXWEEXXEXXKXXASN 252
           G  WN CGN WEE  E  K  ASN
Sbjct: 379 GYRWNYCGNYWEEREERVKAAASN 402

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: 171,679,349
Number of extensions: 6413346
Number of successful extensions: 192
Number of sequences better than 10.0: 1
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 1
Length of query: 139
Length of database: 1,061,185,681
Length adjustment: 103
Effective length of query: 36
Effective length of database: 724,535,537
Effective search space: 26083279332
Effective search space used: 26083279332
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: 29 (15.8 bits)
PSORT 

 psg: 0.90  gvh: 0.62  alm: 0.38  top: 0.60  tms: 0.00  mit: 0.22  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 %: cytoplasmic
	 32.0 %: nuclear
	  8.0 %: mitochondrial
	  4.0 %: extracellular, including cell wall
	  4.0 %: cytoskeletal
	  4.0 %: Golgi

>> prediction for Contig-U04080-1 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) 1
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