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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U01954-1
Contig ID Contig-U01954-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01954-1 (Contig-U01954-1Q) /CSM_Contig/Contig-U01954-1Q.Seq.d
TTCCATTTTTTGTAAACCCCTGGGTTCCCCATTTTTTAGGGGTTTTTTCC
CGCGGTTTTTAAAATGGGGGCCCGCCTTTTCCCCTTTTGGGTTTCCCGGT
TTTCCTTCCTTTTCCCCCCTGGGGATTTGGTGTCCCCAAGGGTTTTCCCC
TGGTGGAATTTTTTCCCGGGGGTTTAATTGGACCTGTTTTAAATTCCCCC
TCCTTTGGTAATTCCCTTTAAATTCTTAATGGTGGGTTTTAAATTTAATT
TAAAACCCCCCAACCACCGGTTTCCTTTGTTCCGGTTTCCTTTGCGGCTT
GCTTTTTGGGTTTAATTGGGGGGGCAATCTTCTTATTATTTTAAAGGGGG
GGTTCAGGGTTTGCCTTTTAAGGTTTGGTTAAGGTTGGGGGTTCTCCCAA
TTTCCCCCCAGGTTACATTTTCATTCCCCCCTTCAAATTTTAACTGGGGT
TCTTCTTTTTTTTTTTTGTTTGTTTCTAAAGGATCCCTATTTAAATTCCC
TTTTCTCTTTTTTTTTTCCTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 588
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 U01954
List of clone(s) 

est1=SSL671Z,1,589
Translated Amino Acid sequence 
fhfl*tpgfpif*gffpavfkmgarlfpfwvsrfsflfppgdlvsprvfpwwnffpgv*l
dlf*ippplvipfkflmvgfkfnlkppnhrfplfrfplrlafwv*LGGQSSYYFKGGVQG
LPFKVWLRLGVLPISPQVTFSFPPSNFNWGSSFFFLFVSKGSLFKFPFLFFFSFLKKKKK
KKKKKKKKKKKKKKKK
Translated Amino Acid sequence (All Frames) 
Frame A:
fhfl*tpgfpif*gffpavfkmgarlfpfwvsrfsflfppgdlvsprvfpwwnffpgv*l
dlf*ippplvipfkflmvgfkfnlkppnhrfplfrfplrlafwv*LGGQSSYYFKGGVQG
LPFKVWLRLGVLPISPQVTFSFPPSNFNWGSSFFFLFVSKGSLFKFPFLFFFSFLKKKKK
KKKKKKKKKKKKKKKK


Frame B:
sifckplgspffrgffprflkwgpafspfgfpgfpsfsplgiwcpqgfspggifsrgfnw
tcfkfpllw*fplns*wwvlnli*nppttgflcsgflcgllfgfnwggnlliilkggfrv
cllrfg*gwgfsqfpprlhfhsplqiltgvllfffclflkdpylnslfsfffpf*kkkkk
kkkkkkkkkkkkkkk


Frame C:
pffvnpwvphflgvfsrgf*nggppfpllgfpvflpfppwgfgvpkgfplveffpgglig
pvlnspsfgnsl*ilnggf*i*fktpqppvsfvpvsfaacflgliggaifllf*rggsgf
af*glvkvggspnfppgyifippfkf*lgffffffvcf*ripi*ipfslffflfkkkkkk
kkkkkkkkkkkkkkk
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U01954-1 (Contig-U01954-1Q)
/CSM_Contig/Contig-U01954-1Q.Seq.d
         (588 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01954-1 (Contig-U01954-1Q) /CSM_Contig/Conti...   613  e-176
Contig-U11643-1 (Contig-U11643-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U04388-1 (Contig-U04388-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U11805-1 (Contig-U11805-1Q) /CSM_Contig/Conti...    36  0.041
Contig-U13904-1 (Contig-U13904-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U13274-1 (Contig-U13274-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U05696-1 (Contig-U05696-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U13437-1 (Contig-U13437-1Q) /CSM_Contig/Conti...    32  0.64
Contig-U12510-1 (Contig-U12510-1Q) /CSM_Contig/Conti...    32  0.64
Contig-U12042-1 (Contig-U12042-1Q) /CSM_Contig/Conti...    32  0.64

>Contig-U01954-1 (Contig-U01954-1Q) /CSM_Contig/Contig-U01954-1Q.Seq.d
          Length = 588

 Score =  613 bits (309), Expect = e-176
 Identities = 361/387 (93%)
 Strand = Plus / Plus

                                                                       
Query: 121 ggggatttggtgtccccaagggttttcccctggtggaattttttcccgggggtttaattg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ggggatttggtgtccccaagggttttcccctggtggaattttttcccgggggtttaattg 180

                                                                       
Query: 181 gacctgttttaaattccccctcctttggtaattccctttaaattcttaatggtgggtttt 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gacctgttttaaattccccctcctttggtaattccctttaaattcttaatggtgggtttt 240

                                                                       
Query: 241 aaatttaatttaaaaccccccaaccaccggtttcctttgttccggtttcctttgcggctt 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aaatttaatttaaaaccccccaaccaccggtttcctttgttccggtttcctttgcggctt 300

                                                                       
Query: 301 gctttttgggtttaattnnnnnnncaatcttcttattattttaaannnnnnnttcagggt 360
           |||||||||||||||||       |||||||||||||||||||||       ||||||||
Sbjct: 301 gctttttgggtttaattgggggggcaatcttcttattattttaaagggggggttcagggt 360

                                                                       
Query: 361 ttgccttttaaggtttggttaaggttgggggttctcccaatttccccccaggttacattt 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 ttgccttttaaggtttggttaaggttgggggttctcccaatttccccccaggttacattt 420

                                                                       
Query: 421 tcattccccccttcaaattttaactggggttcttcnnnnnnnnnnnngtttgtttctaaa 480
           |||||||||||||||||||||||||||||||||||            |||||||||||||
Sbjct: 421 tcattccccccttcaaattttaactggggttcttcttttttttttttgtttgtttctaaa 480

                                      
Query: 481 ggatccctatttaaattcccttttctc 507
           |||||||||||||||||||||||||||
Sbjct: 481 ggatccctatttaaattcccttttctc 507


 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 24/25 (96%)
 Strand = Plus / Minus

                                    
Query: 234 gggttttaaatttaatttaaaaccc 258
           |||||||||||| ||||||||||||
Sbjct: 258 gggttttaaattaaatttaaaaccc 234


>Contig-U11643-1 (Contig-U11643-1Q) /CSM_Contig/Contig-U11643-1Q.Seq.d
          Length = 1826

 Score = 38.2 bits (19), Expect = 0.010
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                               
Query: 237  ttttaaatttaatttaaaa 255
            |||||||||||||||||||
Sbjct: 1773 ttttaaatttaatttaaaa 1791


>Contig-U04388-1 (Contig-U04388-1Q) /CSM_Contig/Contig-U04388-1Q.Seq.d
          Length = 280

 Score = 38.2 bits (19), Expect = 0.010
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 237 ttttaaatttaatttaaaa 255
           |||||||||||||||||||
Sbjct: 242 ttttaaatttaatttaaaa 260


  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: 4484
Number of Sequences: 6905
Number of extensions: 4484
Number of successful extensions: 445
Number of sequences better than 10.0: 132
length of query: 588
length of database: 5,674,871
effective HSP length: 16
effective length of query: 572
effective length of database: 5,564,391
effective search space: 3182831652
effective search space used: 3182831652
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. 5.10
Homology vs DNA 
Query= Contig-U01954-1 (Contig-U01954-1Q) /CSM_Contig/Contig-U01954-1Q.Seq.d
         (588 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

(C93745) Dictyostelium discoideum slug cDNA, clone SSL671.        371   e-171  3
(AC170613) Bos taurus clone CH240-253O4, WORKING DRAFT SEQUE...    48   0.38   1
(AC163475) Bos taurus clone CH240-117G16, WORKING DRAFT SEQU...    48   0.38   1
(AC163058) Bos taurus clone CH240-117K24, WORKING DRAFT SEQU...    48   0.38   1
(DN124455) 1125359 MARC 4PIG Sus scrofa cDNA 3', mRNA sequence.    30   0.62   3
(BU534572) AGENCOURT_10183794 NIH_MGC_143 Mus musculus cDNA ...    42   0.75   2
(AC182160) Bos taurus clone CH240-512A19, WORKING DRAFT SEQU...    36   0.80   2
(AC220234) Bos taurus clone CH240-367B8, WORKING DRAFT SEQUE...    36   0.80   2
(FG757426) G1146P319RJ18.T0 Anolis carolinensis pooled norma...    36   1.4    2
(AC152091) Bos taurus clone CH240-1B10, WORKING DRAFT SEQUEN...    46   1.5    1
(AC166962) Bos taurus clone CH240-85N16, WORKING DRAFT SEQUE...    46   1.5    1
(CL088439) ISB1-10P5_T7.1 ISB1 Xenopus (Silurana) tropicalis...    46   1.5    1
(EL776258) PUND621TVC Pythium ultimum ESTs Pythium ultimum D...    46   1.5    1
(CT853469) Oryza sativa Indica Group EST sequence:OSIGCRN116...    46   1.5    1
(CU466297) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    38   2.2    2
(FG721907) G1144P328RK18.T0 Anolis carolinensis pooled norma...    34   3.5    3
(BM803936) AGENCOURT_6439698 NIH_MGC_71 Homo sapiens cDNA cl...    38   3.5    2
(CK983329) 4109126 BARC 9BOV Bos taurus cDNA clone 9BOV37_L1...    30   3.9    3
(CF243140) AGENCOURT_15111360 NIH_MGC_192 Homo sapiens cDNA ...    32   4.0    2
(DR891527) JGI_XZT19944.rev NIH_XGC_tropTad5 Xenopus (Silura...    34   4.1    2
(BQ583165) E012098-024-006-D11-SP6 MPIZ-ADIS-024-inflorescen...    30   4.3    3
(AC219961) Bos taurus clone CH240-317F22, WORKING DRAFT SEQU...    40   5.4    3
(CR376737) Zebrafish DNA sequence from clone CH211-14G13 in ...    44   5.9    1
(AL929045) Zebrafish DNA sequence from clone CH211-159J13 in...    44   5.9    1
(EA379862) Sequence 28685 from patent US 7314974.                  44   5.9    1
(AF106592) Caenorhabditis elegans cosmid D1037, complete seq...    44   5.9    1
(ER969868) AF__Bc0035N03r AF__Bc Aquilegia formosa genomic, ...    44   5.9    1
(ES342865) CTZ76-G02.y1d-s SHGC-CTZ Ostreococcus lucimarinus...    44   5.9    1
(ES292815) _04X_D01 Bermudagrass Normalized cDNA Library Cyn...    44   5.9    1
(CU550897) Theobroma cacao, mRNA sequence (KZ0ABA10YI17FM1).       44   5.9    1
(FD714303) CAAA18240.rev CAAA Petromyzon marinus Petromyzon ...    44   5.9    1
(EY255996) BF01010A2G02.f1 Normalized subtracted keck librar...    44   5.9    1
(DR886838) JGI_CACY1057.rev NIH_XGC_tropMet6 Xenopus (Silura...    38   6.2    2
(AC214032) Populus trichocarpa clone POP043-I07, complete se...    40   6.9    2
(CX975274) JGI_CAAP9030.fwd NIH_XGC_tropInt1 Xenopus (Silura...    38   7.5    2
(CX975440) JGI_CAAP9119.fwd NIH_XGC_tropInt1 Xenopus (Silura...    38   7.6    2
(AY601894) Melaphis rhois cytochrome b (cytB) gene, partial ...    36   9.2    3

>(C93745) Dictyostelium discoideum slug cDNA, clone SSL671.
          Length = 589

 Score =  357 bits (180), Expect(3) = e-171
 Identities = 180/180 (100%)
 Strand = Plus / Plus


Query: 138 aagggttttcccctggtggaattttttcccgggggtttaattggacctgttttaaattcc 197
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 138 aagggttttcccctggtggaattttttcccgggggtttaattggacctgttttaaattcc 197


Query: 198 ccctcctttggtaattccctttaaattcttaatggtgggttttaaatttaatttaaaacc 257
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 198 ccctcctttggtaattccctttaaattcttaatggtgggttttaaatttaatttaaaacc 257


Query: 258 ccccaaccaccggtttcctttgttccggtttcctttgcggcttgctttttgggtttaatt 317
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 258 ccccaaccaccggtttcctttgttccggtttcctttgcggcttgctttttgggtttaatt 317

 Score =  218 bits (110), Expect(3) = e-171
 Identities = 124/131 (94%)
 Strand = Plus / Plus


Query: 325 caatcttcttattattttaaannnnnnnttcagggtttgccttttaaggtttggttaagg 384
           |||||||||||||||||||||       ||||||||||||||||||||||||||||||||
Sbjct: 325 caatcttcttattattttaaagggggggttcagggtttgccttttaaggtttggttaagg 384


Query: 385 ttgggggttctcccaatttccccccaggttacattttcattccccccttcaaattttaac 444
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 385 ttgggggttctcccaatttccccccaggttacattttcattccccccttcaaattttaac 444


Query: 445 tggggttcttc 455
           |||||||||||
Sbjct: 445 tggggttcttc 455

 Score = 79.8 bits (40), Expect(3) = e-171
 Identities = 40/40 (100%)
 Strand = Plus / Plus


Query: 468 gtttgtttctaaaggatccctatttaaattcccttttctc 507
           ||||||||||||||||||||||||||||||||||||||||
Sbjct: 468 gtttgtttctaaaggatccctatttaaattcccttttctc 507

 Score =  371 bits (187), Expect = 2e-98
 Identities = 201/208 (96%)
 Strand = Plus / Plus


Query: 138 aagggttttcccctggtggaattttttcccgggggtttaattggacctgttttaaattcc 197
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 138 aagggttttcccctggtggaattttttcccgggggtttaattggacctgttttaaattcc 197


Query: 198 ccctcctttggtaattccctttaaattcttaatggtgggttttaaatttaatttaaaacc 257
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 198 ccctcctttggtaattccctttaaattcttaatggtgggttttaaatttaatttaaaacc 257


Query: 258 ccccaaccaccggtttcctttgttccggtttcctttgcggcttgctttttgggtttaatt 317
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 258 ccccaaccaccggtttcctttgttccggtttcctttgcggcttgctttttgggtttaatt 317


Query: 318 nnnnnnncaatcttcttattattttaaa 345
                  |||||||||||||||||||||
Sbjct: 318 gggggggcaatcttcttattattttaaa 345

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 473,796,281
Number of extensions: 28337233
Number of successful extensions: 2287819
Number of sequences better than 10.0: 38
Length of query: 588
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 565
Effective length of database: 99,442,330,388
Effective search space: 56184916669220
Effective search space used: 56184916669220
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01954-1 (Contig-U01954-1Q) /CSM_Contig/Contig-U01954-1Q.Seq.d
         (588 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AF406972_1(AF406972|pid:none) Mycoplasma bovis variable surface ...    33   7.5
AF332093_459(AF332093|pid:none) White spot syndrome virus, compl...    33   7.5
BC122272_1(BC122272|pid:none) Danio rerio zgc:153405, mRNA (cDNA...    30   7.8
CP000148_3000(CP000148|pid:none) Geobacter metallireducens GS-15...    32   9.8
EU581950_1(EU581950|pid:none) Brassica oleracea clone BAC B67C16...    32   9.9
AY061259_1(AY061259|pid:none) Drosophila melanogaster LD19086 fu...    32   9.9
CP001087_2365(CP001087|pid:none) Desulfobacterium autotrophicum ...    32   9.9

>AF406972_1(AF406972|pid:none) Mycoplasma bovis variable surface
           lipoprotein Vsp422-1 gene, complete cds.
          Length = 229

 Score = 32.7 bits (73), Expect = 7.5
 Identities = 19/55 (34%), Positives = 27/55 (49%)
 Frame = -2

Query: 170 PGKKFHQGKTLGDTKSPGGKRKENRETQKGKRRAPILKTAGKNP*KMGNPGVYKK 6
           PG   + G+     K+PGG +     T+ GK  +  ++  GKNP    NPG  KK
Sbjct: 52  PGGDKNPGQNTDPGKNPGGDKNPGGNTEPGKNPSENIE-PGKNPGGDKNPGTDKK 105

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: 880,274,669
Number of extensions: 17957015
Number of successful extensions: 57345
Number of sequences better than 10.0: 7
Number of HSP's gapped: 56972
Number of HSP's successfully gapped: 8
Length of query: 196
Length of database: 1,051,180,864
Length adjustment: 122
Effective length of query: 74
Effective length of database: 656,320,666
Effective search space: 48567729284
Effective search space used: 48567729284
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: 30 (16.2 bits)
PSORT 

 psg: 0.84  gvh: 0.61  alm: 0.38  top: 0.53  tms: 0.00  mit: 0.36  mip: 0.00
 nuc: 1.38  erl: 0.00  erm: 0.80  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 

	 68.0 %: nuclear
	 20.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U01954-1 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